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From gandhira...@apache.org
Subject svn commit: r1815709 [1/2] - in /ctakes/trunk: ./ ctakes-assertion/ ctakes-temporal/ ctakes-type-system/ ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/ ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/ ctakes-ytex-web/...
Date Sun, 19 Nov 2017 08:00:56 GMT
Author: gandhirajan
Date: Sun Nov 19 08:00:56 2017
New Revision: 1815709

URL: http://svn.apache.org/viewvc?rev=1815709&view=rev
Log:
CTAKES-472: Upgrade Spring dependency from 3.1.2 to 4.x This upgrade helps in enabling REST support in cTAKES

Modified:
    ctakes/trunk/ctakes-assertion/build.xml
    ctakes/trunk/ctakes-assertion/pom.xml
    ctakes/trunk/ctakes-temporal/pom.xml
    ctakes/trunk/ctakes-type-system/pom.xml
    ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/DBCollectionReader.java
    ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DBConsumerTest.java
    ctakes/trunk/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/ConceptSearchServiceImpl.java
    ctakes/trunk/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/DocumentSearchServiceImpl.java
    ctakes/trunk/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/DocumentViewBean.java
    ctakes/trunk/ctakes-ytex/pom.xml
    ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/AbstractBagOfWordsExporter.java
    ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SparseDataExporterImpl.java
    ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/CorpusKernelEvaluatorImpl.java
    ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/tree/InstanceTreeBuilderImpl.java
    ctakes/trunk/pom.xml

Modified: ctakes/trunk/ctakes-assertion/build.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/build.xml?rev=1815709&r1=1815708&r2=1815709&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/build.xml (original)
+++ ctakes/trunk/ctakes-assertion/build.xml Sun Nov 19 08:00:56 2017
@@ -1,393 +1,393 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<!--
-
-    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.
-
--->
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-              Any modifications will be overwritten.
-              To include a user specific buildfile here, simply create one in the same
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-            <classpath refid="run.ctakes_assertion_crossvalidation.classpath"/>
-        </java>
-    </target>
-    <target name="ctakes__assertion_eval_preprocess">
-        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
-            <arg line="--train-dir data/train --test-dir data/test --models-dir data/model/eval.model --dev-dir data/dev --preprocess-only &quot;H:\SHARP\Corpora\\Mayo\UMLS_CEM&quot;"/>
-            <classpath refid="run.ctakes__assertion_eval_preprocess.classpath"/>
-        </java>
-    </target>
-    <target name="ctakes__assertion_eval">
-        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
-            <arg line="--train-dir data/train --test-dir data/test --models-dir data/model/eval.model --dev-dir data/dev"/>
-            <classpath refid="run.ctakes__assertion_eval.classpath"/>
-        </java>
-    </target>
-    <target name="ctakes_assertion_read_gold_and_preprocess">
-        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
-            <jvmarg line="-Xmx3g"/>
-            <arg line="--train-dir sharp_data/train --test-dir sharp_data/test --dev-dir sharp_data/dev --models-dir sharp_data/model/eval.model --preprocess-only &quot;/Users/m081914/work/data/sharp/Seed Corpus/Mayo/UMLS_CEM&quot;"/>
-            <classpath refid="run.ctakes_assertion_read_gold_and_preprocess.classpath"/>
-        </java>
-    </target>
-    <target name="ctakes_assertion_evaluation_on_test">
-        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
-            <jvmarg line="-Xmx3g"/>
-            <arg line="--train-dir sharp_data/train --test-dir sharp_data/test --models-dir sharp_data/model/eval.model"/>
-            <classpath refid="run.ctakes_assertion_evaluation_on_test.classpath"/>
-        </java>
-    </target>
-    <target name="ctakes_assertion_evaluation_on_output">
-        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
-            <jvmarg line="-Xmx3g"/>
-            <arg line="--train-dir sharp_data/train --test-dir sharp_data/dev --models-dir sharp_data/model/eval.model --evaluation-output-dir sharp_data/output_instancegathering --eval-only"/>
-            <classpath refid="run.ctakes_assertion_evaluation_on_output.classpath"/>
-        </java>
-    </target>
-    <target name="ctakes_assertion_crossvalidation">
-        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
-            <jvmarg line="-Xmx3g"/>
-            <arg line="--train-dir /Users/m081914/work/data/assertion/fromtim_sharp_data/train --models-dir ../ctakes-assertion-res/resources/model/sharptrain-xval --cross-validation 5"/>
-            <classpath refid="run.ctakes_assertion_crossvalidation.classpath"/>
-        </java>
-    </target>
-    <target name="ctakes__assertion_eval_preprocess">
-        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
-            <arg line="--train-dir data/train --test-dir data/test --models-dir data/model/eval.model --dev-dir data/dev --preprocess-only &quot;H:\SHARP\Corpora\\Mayo\UMLS_CEM&quot;"/>
-            <classpath refid="run.ctakes__assertion_eval_preprocess.classpath"/>
-        </java>
-    </target>
-    <target name="ctakes__assertion_eval">
-        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
-            <arg line="--train-dir data/train --test-dir data/test --models-dir data/model/eval.model --dev-dir data/dev"/>
-            <classpath refid="run.ctakes__assertion_eval.classpath"/>
-        </java>
-    </target>
-    <target name="PolarityCotrainingTrain">
-        <java classname="org.apache.ctakes.assertion.train.PolarityCotrainingTrain" failonerror="true" fork="yes">
-            <classpath refid="run.PolarityCotrainingTrain.classpath"/>
-        </java>
-    </target>
-    <target name="PolarityCotrainingTests">
-        <java classname="org.apache.ctakes.assertion.train.PolarityCotrainingTests" failonerror="true" fork="yes">
-            <classpath refid="run.PolarityCotrainingTests.classpath"/>
-        </java>
-    </target>
-</project>
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!--
+
+    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.
+
+-->
+<!-- WARNING: Eclipse auto-generated file.
+              Any modifications will be overwritten.
+              To include a user specific buildfile here, simply create one in the same
+              directory with the processing instruction <?eclipse.ant.import?>
+              as the first entry and export the buildfile again. --><project basedir="." default="build" name="ctakes-assertion">
+    <property environment="env"/>
+    <property name="ECLIPSE_HOME" value="../../../tools/eclipse"/>
+    <property name="debuglevel" value="source,lines,vars"/>
+    <property name="target" value="1.6"/>
+    <property name="source" value="1.6"/>
+    <path id="UIMA.userclasspath"/>
+    <path id="Maven Dependencies.libraryclasspath">
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+        <pathelement location="../../../../../../ctakes-dictionary-lookup-res"/>
+        <pathelement location="../../../../.m2/repository/hsqldb/hsqldb/1.8.0.10/hsqldb-1.8.0.10.jar"/>
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+        <pathelement location="../../../../.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-umls2011ab/3.1.0/ctakes-resources-umls2011ab-3.1.0.jar"/>
+        <pathelement location="../../../../../../ctakes-core"/>
+        <pathelement location="../../../../../../ctakes-core-res"/>
+        <pathelement location="../../../../.m2/repository/org/jdom/jdom2/2.0.3/jdom2-2.0.3.jar"/>
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+        <pathelement location="../../../../.m2/repository/com/googlecode/armbrust-file-utils/sqlwrapper/0.0.1/sqlwrapper-0.0.1.jar"/>
+        <pathelement location="../../../../.m2/repository/net/sourceforge/openai/openaifsm/0.0.1/openaifsm-0.0.1.jar"/>
+        <pathelement location="../../../../../../ctakes-constituency-parser"/>
+        <pathelement location="../../../../../../ctakes-constituency-parser-res"/>
+        <pathelement location="../../../../../../ctakes-utils"/>
+        <pathelement location="../../../../../../ctakes-pos-tagger"/>
+        <pathelement location="../../../../../../ctakes-pos-tagger-res"/>
+        <pathelement location="../../../../.m2/repository/com/googlecode/clearnlp/clearnlp/1.3.1/clearnlp-1.3.1.jar"/>
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+        <pathelement location="../../../../.m2/repository/org/tukaani/xz/1.0/xz-1.0.jar"/>
+        <pathelement location="../../../../.m2/repository/net/sourceforge/jregex/jregex/1.2_01/jregex-1.2_01.jar"/>
+        <pathelement location="../../../../../../ctakes-dependency-parser"/>
+        <pathelement location="../../../../../../ctakes-dependency-parser-res"/>
+        <pathelement location="../../../../.m2/repository/org/cleartk/cleartk-ml/1.3.0/cleartk-ml-1.3.0.jar"/>
+        <pathelement location="../../../../.m2/repository/org/cleartk/cleartk-ml-libsvm/1.2.0/cleartk-ml-libsvm-1.2.0.jar"/>
+        <pathelement location="../../../../.m2/repository/de/bwaldvogel/liblinear/1.92/liblinear-1.92.jar"/>
+        <pathelement location="../../../../.m2/repository/org/cleartk/cleartk-ml-opennlp-maxent/1.1.2/cleartk-ml-opennlp-maxent-1.1.2.jar"/>
+        <pathelement location="../../../../.m2/repository/org/cleartk/cleartk-util/0.9.2/cleartk-util-0.9.2.jar"/>
+        <pathelement location="../../../../.m2/repository/org/cleartk/cleartk-eval/0.9.2/cleartk-eval-0.9.2.jar"/>
+        <pathelement location="../../../../.m2/repository/args4j/args4j/2.0.16/args4j-2.0.16.jar"/>
+        <pathelement location="../../../../.m2/repository/commons-io/commons-io/2.0.1/commons-io-2.0.1.jar"/>
+        <pathelement location="../../../../.m2/repository/commons-lang/commons-lang/2.4/commons-lang-2.4.jar"/>
+        <pathelement location="../../../../.m2/repository/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar"/>
+        <pathelement location="../../../../.m2/repository/com/google/guava/guava/10.0/guava-10.0.jar"/>
+        <pathelement location="../../../../.m2/repository/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar"/>
+        <pathelement location="../../../../.m2/repository/commons-cli/commons-cli/1.2/commons-cli-1.2.jar"/>
+        <pathelement location="../../../../.m2/repository/com/carrotsearch/hppc/0.4.1/hppc-0.4.1.jar"/>
+        <pathelement location="../../../../.m2/repository/jdom/jdom/1.0/jdom-1.0.jar"/>
+        <pathelement location="../../../../.m2/repository/junit/junit/4.10/junit-4.10.jar"/>
+        <pathelement location="../../../../.m2/repository/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"/>
+        <pathelement location="../../../../.m2/repository/log4j/log4j/1.2.16/log4j-1.2.16.jar"/>
+        <pathelement location="../../../../.m2/repository/org/apache/opennlp/opennlp-maxent/3.0.2-incubating/opennlp-maxent-3.0.2-incubating.jar"/>
+        <pathelement location="../../../../.m2/repository/org/apache/opennlp/opennlp-tools/1.5.2-incubating/opennlp-tools-1.5.2-incubating.jar"/>
+        <pathelement location="../../../../.m2/repository/jwnl/jwnl/1.3.3/jwnl-1.3.3.jar"/>
+        <pathelement location="../../../../.m2/repository/org/apache/lucene/lucene-core/4.0.0/lucene-core-4.0.0.jar"/>
+        <pathelement location="../../../../.m2/repository/tw/edu/ntu/csie/libsvm/3.1/libsvm-3.1.jar"/>
+        <pathelement location="../../../../.m2/repository/org/springframework/spring-core/4.3.12.RELEASE/spring-core-4.3.12.RELEASE.jar"/>
+        <pathelement location="../../../../.m2/repository/org/springframework/spring-asm/4.3.12.RELEASE/spring-asm-4.3.12.RELEASE.jar"/>
+        <pathelement location="../../../../.m2/repository/org/uimafit/uimafit/1.4.0/uimafit-1.4.0.jar"/>
+        <pathelement location="../../../../.m2/repository/org/apache/uima/uimaj-tools/2.4.0/uimaj-tools-2.4.0.jar"/>
+        <pathelement location="../../../../.m2/repository/org/apache/uima/uimaj-cpe/2.4.0/uimaj-cpe-2.4.0.jar"/>
+        <pathelement location="../../../../.m2/repository/org/apache/uima/uimaj-adapter-vinci/2.4.0/uimaj-adapter-vinci-2.4.0.jar"/>
+        <pathelement location="../../../../.m2/repository/org/apache/uima/jVinci/2.4.0/jVinci-2.4.0.jar"/>
+        <pathelement location="../../../../.m2/repository/org/apache/uima/uimaj-document-annotation/2.4.0/uimaj-document-annotation-2.4.0.jar"/>
+        <pathelement location="../../../../.m2/repository/org/springframework/spring-context/3.1.0.RELEASE/spring-context-3.1.0.RELEASE.jar"/>
+        <pathelement location="../../../../.m2/repository/org/springframework/spring-aop/3.1.0.RELEASE/spring-aop-3.1.0.RELEASE.jar"/>
+        <pathelement location="../../../../.m2/repository/aopalliance/aopalliance/1.0/aopalliance-1.0.jar"/>
+        <pathelement location="../../../../.m2/repository/org/springframework/spring-beans/3.1.0.RELEASE/spring-beans-3.1.0.RELEASE.jar"/>
+        <pathelement location="../../../../.m2/repository/org/springframework/spring-expression/3.1.0.RELEASE/spring-expression-3.1.0.RELEASE.jar"/>
+        <pathelement location="../../../../.m2/repository/org/codehaus/jackson/jackson-core-asl/1.5.0/jackson-core-asl-1.5.0.jar"/>
+        <pathelement location="../../../../.m2/repository/org/codehaus/jackson/jackson-mapper-asl/1.5.0/jackson-mapper-asl-1.5.0.jar"/>
+        <pathelement location="../../../../.m2/repository/org/scala-lang/scala-library/2.9.0/scala-library-2.9.0.jar"/>
+        <pathelement location="../../../../.m2/repository/org/scala-tools/sbinary/sbinary_2.9.0/0.4.0/sbinary_2.9.0-0.4.0.jar"/>
+        <pathelement location="../../../../../../ctakes-lvg"/>
+        <pathelement location="../../../../../../ctakes-lvg-res"/>
+        <pathelement location="../../../../.m2/repository/gov/nih/nlm/nls/lvg/lvg2010dist/0.0.1/lvg2010dist-0.0.1.jar"/>
+        <pathelement location="../../../../../../ctakes-context-tokenizer"/>
+        <pathelement location="../../../../../../ctakes-chunker"/>
+        <pathelement location="../../../../../../ctakes-chunker-res"/>
+    </path>
+    <path id="ctakes-assertion.classpath">
+        <pathelement location="target/classes"/>
+        <path refid="UIMA.userclasspath"/>
+        <pathelement location="target/test-classes"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.CrossValidateAttributeModels.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.CrossValidateChi2GridSearch.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.NegExCorpusReader.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.ReadAndPreprocessForAttributeModels.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.TestAttributeModels.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.TestFeatureSelection.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.TrainAttributeModels.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.ctakes_assertion_read_gold_and_preprocess.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.ctakes_assertion_evaluation_on_test.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.ctakes_assertion_evaluation_on_output.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.ctakes_assertion_crossvalidation.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.ctakes__assertion_eval_preprocess.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.ctakes__assertion_eval.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.ctakes_assertion_read_gold_and_preprocess.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.ctakes_assertion_evaluation_on_test.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.ctakes_assertion_evaluation_on_output.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.ctakes_assertion_crossvalidation.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.ctakes__assertion_eval_preprocess.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.ctakes__assertion_eval.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.PolarityCotrainingTrain.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <path id="run.PolarityCotrainingTests.classpath">
+        <path refid="ctakes-assertion.classpath"/>
+        <path refid="Maven Dependencies.libraryclasspath"/>
+    </path>
+    <target name="init">
+        <mkdir dir="target/classes"/>
+        <mkdir dir="target/test-classes"/>
+        <copy includeemptydirs="false" todir="target/classes">
+            <fileset dir="src/main/java">
+                <exclude name="**/*.java"/>
+            </fileset>
+        </copy>
+        <copy includeemptydirs="false" todir="target/classes">
+            <fileset dir="src/main/resources">
+                <exclude name="**/*.java"/>
+                <exclude name="**"/>
+            </fileset>
+        </copy>
+        <copy includeemptydirs="false" todir="target/test-classes">
+            <fileset dir="src/test/java">
+                <exclude name="**/*.java"/>
+            </fileset>
+        </copy>
+        <copy includeemptydirs="false" todir="target/classes">
+            <fileset dir="target/generated-sources/jcasgen">
+                <exclude name="**/*.java"/>
+            </fileset>
+        </copy>
+    </target>
+    <target name="clean">
+        <delete dir="target/classes"/>
+        <delete dir="target/test-classes"/>
+    </target>
+    <target depends="clean" name="cleanall"/>
+    <target depends="build-subprojects,build-project" name="build"/>
+    <target name="build-subprojects"/>
+    <target depends="init" name="build-project">
+        <echo message="${ant.project.name}: ${ant.file}"/>
+        <javac debug="true" debuglevel="${debuglevel}" destdir="target/classes" includeantruntime="false" source="${source}" target="${target}">
+            <src path="src/main/java"/>
+            <src path="src/main/resources"/>
+            <src path="target/generated-sources/jcasgen"/>
+            <exclude name="**"/>
+            <classpath refid="ctakes-assertion.classpath"/>
+        </javac>
+        <javac debug="true" debuglevel="${debuglevel}" destdir="target/test-classes" includeantruntime="false" source="${source}" target="${target}">
+            <src path="src/test/java"/>
+            <classpath refid="ctakes-assertion.classpath"/>
+        </javac>
+    </target>
+    <target description="Build all projects which reference this project. Useful to propagate changes." name="build-refprojects"/>
+    <target description="copy Eclipse compiler jars to ant lib directory" name="init-eclipse-compiler">
+        <copy todir="${ant.library.dir}">
+            <fileset dir="${ECLIPSE_HOME}/plugins" includes="org.eclipse.jdt.core_*.jar"/>
+        </copy>
+        <unzip dest="${ant.library.dir}">
+            <patternset includes="jdtCompilerAdapter.jar"/>
+            <fileset dir="${ECLIPSE_HOME}/plugins" includes="org.eclipse.jdt.core_*.jar"/>
+        </unzip>
+    </target>
+    <target description="compile project with Eclipse compiler" name="build-eclipse-compiler">
+        <property name="build.compiler" value="org.eclipse.jdt.core.JDTCompilerAdapter"/>
+        <antcall target="build"/>
+    </target>
+    <target name="CrossValidateAttributeModels">
+        <java classname="org.apache.ctakes.assertion.train.CrossValidateAttributeModels" failonerror="true" fork="yes">
+            <jvmarg line="-Xmx3g"/>
+            <classpath refid="run.CrossValidateAttributeModels.classpath"/>
+        </java>
+    </target>
+    <target name="CrossValidateChi2GridSearch">
+        <java classname="org.apache.ctakes.assertion.train.CrossValidateChi2GridSearch" failonerror="true" fork="yes">
+            <jvmarg line="-Xmx2g"/>
+            <classpath refid="run.CrossValidateChi2GridSearch.classpath"/>
+        </java>
+    </target>
+    <target name="NegExCorpusReader">
+        <java classname="org.apache.ctakes.assertion.cr.NegExCorpusReader" failonerror="true" fork="yes">
+            <arg line="/Users/m081914/work/data/negextestset/rsAnnotations-1-120-random.txt"/>
+            <classpath refid="run.NegExCorpusReader.classpath"/>
+        </java>
+    </target>
+    <target name="ReadAndPreprocessForAttributeModels">
+        <java classname="org.apache.ctakes.assertion.train.ReadAndPreprocessForAttributeModels" failonerror="true" fork="yes">
+            <jvmarg line="-Xmx2g"/>
+            <classpath refid="run.ReadAndPreprocessForAttributeModels.classpath"/>
+        </java>
+    </target>
+    <target name="TestAttributeModels">
+        <java classname="org.apache.ctakes.assertion.train.TestAttributeModels" failonerror="true" fork="yes">
+            <classpath refid="run.TestAttributeModels.classpath"/>
+        </java>
+    </target>
+    <target name="TestFeatureSelection">
+        <java classname="org.apache.ctakes.assertion.eval.TestFeatureSelection" failonerror="true" fork="yes">
+            <classpath refid="run.TestFeatureSelection.classpath"/>
+        </java>
+    </target>
+    <target name="TrainAttributeModels">
+        <java classname="org.apache.ctakes.assertion.train.TrainAttributeModels" failonerror="true" fork="yes">
+            <jvmarg line="-Xmx3g"/>
+            <classpath refid="run.TrainAttributeModels.classpath"/>
+        </java>
+    </target>
+    <target name="ctakes_assertion_read_gold_and_preprocess">
+        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
+            <jvmarg line="-Xmx3g"/>
+            <arg line="--train-dir sharp_data/train --test-dir sharp_data/test --dev-dir sharp_data/dev --models-dir sharp_data/model/eval.model --preprocess-only &quot;/Users/m081914/work/data/sharp/Seed Corpus/Mayo/UMLS_CEM&quot;"/>
+            <classpath refid="run.ctakes_assertion_read_gold_and_preprocess.classpath"/>
+        </java>
+    </target>
+    <target name="ctakes_assertion_evaluation_on_test">
+        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
+            <jvmarg line="-Xmx3g"/>
+            <arg line="--train-dir sharp_data/train --test-dir sharp_data/test --models-dir sharp_data/model/eval.model"/>
+            <classpath refid="run.ctakes_assertion_evaluation_on_test.classpath"/>
+        </java>
+    </target>
+    <target name="ctakes_assertion_evaluation_on_output">
+        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
+            <jvmarg line="-Xmx3g"/>
+            <arg line="--train-dir sharp_data/train --test-dir sharp_data/dev --models-dir sharp_data/model/eval.model --evaluation-output-dir sharp_data/output_instancegathering --eval-only"/>
+            <classpath refid="run.ctakes_assertion_evaluation_on_output.classpath"/>
+        </java>
+    </target>
+    <target name="ctakes_assertion_crossvalidation">
+        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
+            <jvmarg line="-Xmx3g"/>
+            <arg line="--train-dir /Users/m081914/work/data/assertion/fromtim_sharp_data/train --models-dir ../ctakes-assertion-res/resources/model/sharptrain-xval --cross-validation 5"/>
+            <classpath refid="run.ctakes_assertion_crossvalidation.classpath"/>
+        </java>
+    </target>
+    <target name="ctakes__assertion_eval_preprocess">
+        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
+            <arg line="--train-dir data/train --test-dir data/test --models-dir data/model/eval.model --dev-dir data/dev --preprocess-only &quot;H:\SHARP\Corpora\\Mayo\UMLS_CEM&quot;"/>
+            <classpath refid="run.ctakes__assertion_eval_preprocess.classpath"/>
+        </java>
+    </target>
+    <target name="ctakes__assertion_eval">
+        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
+            <arg line="--train-dir data/train --test-dir data/test --models-dir data/model/eval.model --dev-dir data/dev"/>
+            <classpath refid="run.ctakes__assertion_eval.classpath"/>
+        </java>
+    </target>
+    <target name="ctakes_assertion_read_gold_and_preprocess">
+        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
+            <jvmarg line="-Xmx3g"/>
+            <arg line="--train-dir sharp_data/train --test-dir sharp_data/test --dev-dir sharp_data/dev --models-dir sharp_data/model/eval.model --preprocess-only &quot;/Users/m081914/work/data/sharp/Seed Corpus/Mayo/UMLS_CEM&quot;"/>
+            <classpath refid="run.ctakes_assertion_read_gold_and_preprocess.classpath"/>
+        </java>
+    </target>
+    <target name="ctakes_assertion_evaluation_on_test">
+        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
+            <jvmarg line="-Xmx3g"/>
+            <arg line="--train-dir sharp_data/train --test-dir sharp_data/test --models-dir sharp_data/model/eval.model"/>
+            <classpath refid="run.ctakes_assertion_evaluation_on_test.classpath"/>
+        </java>
+    </target>
+    <target name="ctakes_assertion_evaluation_on_output">
+        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
+            <jvmarg line="-Xmx3g"/>
+            <arg line="--train-dir sharp_data/train --test-dir sharp_data/dev --models-dir sharp_data/model/eval.model --evaluation-output-dir sharp_data/output_instancegathering --eval-only"/>
+            <classpath refid="run.ctakes_assertion_evaluation_on_output.classpath"/>
+        </java>
+    </target>
+    <target name="ctakes_assertion_crossvalidation">
+        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
+            <jvmarg line="-Xmx3g"/>
+            <arg line="--train-dir /Users/m081914/work/data/assertion/fromtim_sharp_data/train --models-dir ../ctakes-assertion-res/resources/model/sharptrain-xval --cross-validation 5"/>
+            <classpath refid="run.ctakes_assertion_crossvalidation.classpath"/>
+        </java>
+    </target>
+    <target name="ctakes__assertion_eval_preprocess">
+        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
+            <arg line="--train-dir data/train --test-dir data/test --models-dir data/model/eval.model --dev-dir data/dev --preprocess-only &quot;H:\SHARP\Corpora\\Mayo\UMLS_CEM&quot;"/>
+            <classpath refid="run.ctakes__assertion_eval_preprocess.classpath"/>
+        </java>
+    </target>
+    <target name="ctakes__assertion_eval">
+        <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
+            <arg line="--train-dir data/train --test-dir data/test --models-dir data/model/eval.model --dev-dir data/dev"/>
+            <classpath refid="run.ctakes__assertion_eval.classpath"/>
+        </java>
+    </target>
+    <target name="PolarityCotrainingTrain">
+        <java classname="org.apache.ctakes.assertion.train.PolarityCotrainingTrain" failonerror="true" fork="yes">
+            <classpath refid="run.PolarityCotrainingTrain.classpath"/>
+        </java>
+    </target>
+    <target name="PolarityCotrainingTests">
+        <java classname="org.apache.ctakes.assertion.train.PolarityCotrainingTests" failonerror="true" fork="yes">
+            <classpath refid="run.PolarityCotrainingTests.classpath"/>
+        </java>
+    </target>
+</project>

Modified: ctakes/trunk/ctakes-assertion/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/pom.xml?rev=1815709&r1=1815708&r2=1815709&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/pom.xml (original)
+++ ctakes/trunk/ctakes-assertion/pom.xml Sun Nov 19 08:00:56 2017
@@ -1,175 +1,175 @@
-<?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>
-	<artifactId>ctakes-assertion</artifactId>
-	<name>Apache cTAKES Assertion</name>
-	<parent>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes</artifactId>
-		<version>4.0.1-SNAPSHOT</version>
-	</parent>
-	<dependencies>
-	<dependency>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes-assertion-res</artifactId>
-	</dependency>
-        <!--  Core added by Constituency parser, context tokenizer, chunker and dependency parser (via pos tagger).  -->
-        <!--<dependency>-->
-        <!--<groupId>org.apache.ctakes</groupId>-->
-        <!--<artifactId>ctakes-core</artifactId>-->
-        <!--</dependency>-->
-    <dependency>
-      <groupId>org.apache.ctakes</groupId>
-      <artifactId>ctakes-constituency-parser</artifactId>
-    </dependency>
-        <!--  pos tagger added by Dependency parser and Chunker.  -->
-        <!--<dependency>-->
-        <!--<groupId>org.apache.ctakes</groupId>-->
-        <!--<artifactId>ctakes-pos-tagger</artifactId>-->
-        <!--</dependency>-->
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-dependency-parser</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.cleartk</groupId>
-			<artifactId>cleartk-ml-libsvm</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.cleartk</groupId>
-			<artifactId>cleartk-ml-opennlp-maxent</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.cleartk</groupId>
-			<artifactId>cleartk-eval</artifactId>
-		</dependency>
-        <!--  args4j added by dependency parser.  -->
-        <!--<dependency>-->
-        <!--<groupId>args4j</groupId>-->
-        <!--<artifactId>args4j</artifactId>-->
-        <!--</dependency>-->
-        <!--  commons-lang added by dependency parser.  -->
-        <!--<dependency>-->
-        <!--<groupId>commons-lang</groupId>-->
-        <!--<artifactId>commons-lang</artifactId>-->
-        <!--</dependency>-->
-        <!--  commons-lang added by dependency parser.  -->
-        <!--<dependency>-->
-        <!--<groupId>commons-logging</groupId>-->
-        <!--<artifactId>commons-logging</artifactId>-->
-        <!--</dependency>-->
-		<dependency>
-			<groupId>commons-cli</groupId>
-			<artifactId>commons-cli</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>com.carrotsearch</groupId>
-			<artifactId>hppc</artifactId>
-		</dependency>
-        <!--  lucene core added by dependency parser.  -->
-        <!--<dependency>-->
-        <!--<groupId>org.apache.lucene</groupId>-->
-        <!--<artifactId>lucene-core</artifactId>-->
-        <!--</dependency>-->
-		<dependency>
-            <groupId>org.apache.uima</groupId>
-            <artifactId>uimaj-document-annotation</artifactId>
-            <version>2.9.0</version>
-		</dependency>
-        <!--  libsvm added by type system.  -->
-        <!--<dependency>-->
-        <!--<groupId>tw.edu.ntu.csie</groupId>-->
-        <!--<artifactId>libsvm</artifactId>-->
-        <!--</dependency>-->
-		<dependency>
-			<groupId>org.springframework</groupId>
-			<artifactId>spring-core</artifactId>
-		</dependency>
-		<!-- we excluded spring-context uimafit transitive dependency in the parent pom, include it here -->
-		<dependency>
-			<groupId>org.springframework</groupId>
-			<artifactId>spring-context</artifactId>
-		</dependency>
-
-		<dependency>
-			<groupId>org.codehaus.jackson</groupId>
-			<artifactId>jackson-core-asl</artifactId>
-			<version>1.5.0</version>
-		</dependency>
-		<dependency>
-			<groupId>org.codehaus.jackson</groupId>
-			<artifactId>jackson-mapper-asl</artifactId>
-			<version>1.5.0</version>
-		</dependency>
-
-		<dependency>
-			<groupId>org.scala-tools.sbinary</groupId>
-			<artifactId>sbinary_2.9.0</artifactId>
-			<version>0.4.0</version>
-		</dependency>
-        <!--  LVG added by dependency parser.  -->
-        <!--<dependency>-->
-        <!--<groupId>org.apache.ctakes</groupId>-->
-        <!--<artifactId>ctakes-lvg</artifactId>-->
-        <!--</dependency>-->
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-context-tokenizer</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-chunker</artifactId>
-		</dependency>
-        <!--  assertion does not depend upon ctakes-relation-extractor.  It uses relation types in:
-         JudgeAttributeInstances and MiPACQKnowtatorXMLReader -->
-        <!--<dependency>-->
-        <!--<groupId>org.apache.ctakes</groupId>-->
-        <!--<artifactId>ctakes-relation-extractor</artifactId>-->
-        <!--</dependency>-->
-		<dependency>
-			<groupId>org.cleartk</groupId>
-			<artifactId>cleartk-ml-liblinear</artifactId>
-		</dependency>
-	</dependencies>	 	
-	<build>
-		<plugins>
-				<plugin>
-				  <groupId>org.apache.uima</groupId>
-				  <artifactId>jcasgen-maven-plugin</artifactId>
-				  <version>2.9.0</version>				  
-				  <executions>
-				    <execution>
-				      <goals><goal>generate</goal></goals>
-				      <configuration>
-				        <typeSystemIncludes>
-                            <typeSystemInclude>src/main/resources/org/apache/ctakes/**/types/TypeSystem.xml
-                            </typeSystemInclude>
-				        </typeSystemIncludes>
-                          <limitToProject>true</limitToProject>
-				      </configuration>
-				    </execution>
-				    </executions>
-				</plugin>
-		</plugins>				
- 	</build>	
-</project>
+<?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>
+	<artifactId>ctakes-assertion</artifactId>
+	<name>Apache cTAKES Assertion</name>	
+	<parent>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes</artifactId>
+		<version>4.0.1-SNAPSHOT</version>
+	</parent>
+	<dependencies>
+	<dependency>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes-assertion-res</artifactId>
+	</dependency>
+        <!--  Core added by Constituency parser, context tokenizer, chunker and dependency parser (via pos tagger).  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-core</artifactId>-->
+        <!--</dependency>-->
+    <dependency>
+      <groupId>org.apache.ctakes</groupId>
+      <artifactId>ctakes-constituency-parser</artifactId>
+    </dependency>
+        <!--  pos tagger added by Dependency parser and Chunker.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-pos-tagger</artifactId>-->
+        <!--</dependency>-->
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-dependency-parser</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.cleartk</groupId>
+			<artifactId>cleartk-ml-libsvm</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.cleartk</groupId>
+			<artifactId>cleartk-ml-opennlp-maxent</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.cleartk</groupId>
+			<artifactId>cleartk-eval</artifactId>
+		</dependency>
+        <!--  args4j added by dependency parser.  -->
+        <!--<dependency>-->
+        <!--<groupId>args4j</groupId>-->
+        <!--<artifactId>args4j</artifactId>-->
+        <!--</dependency>-->
+        <!--  commons-lang added by dependency parser.  -->
+        <!--<dependency>-->
+        <!--<groupId>commons-lang</groupId>-->
+        <!--<artifactId>commons-lang</artifactId>-->
+        <!--</dependency>-->
+        <!--  commons-lang added by dependency parser.  -->
+        <!--<dependency>-->
+        <!--<groupId>commons-logging</groupId>-->
+        <!--<artifactId>commons-logging</artifactId>-->
+        <!--</dependency>-->
+		<dependency>
+			<groupId>commons-cli</groupId>
+			<artifactId>commons-cli</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.carrotsearch</groupId>
+			<artifactId>hppc</artifactId>
+		</dependency>
+        <!--  lucene core added by dependency parser.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.lucene</groupId>-->
+        <!--<artifactId>lucene-core</artifactId>-->
+        <!--</dependency>-->
+		<dependency>
+            <groupId>org.apache.uima</groupId>
+            <artifactId>uimaj-document-annotation</artifactId>
+            <version>2.9.0</version>
+		</dependency>
+        <!--  libsvm added by type system.  -->
+        <!--<dependency>-->
+        <!--<groupId>tw.edu.ntu.csie</groupId>-->
+        <!--<artifactId>libsvm</artifactId>-->
+        <!--</dependency>-->
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-core</artifactId>			
+		</dependency>
+		<!-- we excluded spring-context uimafit transitive dependency in the parent pom, include it here -->
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-context</artifactId>			
+		</dependency>
+
+		<dependency>
+			<groupId>org.codehaus.jackson</groupId>
+			<artifactId>jackson-core-asl</artifactId>
+			<version>1.5.0</version>
+		</dependency>
+		<dependency>
+			<groupId>org.codehaus.jackson</groupId>
+			<artifactId>jackson-mapper-asl</artifactId>
+			<version>1.5.0</version>
+		</dependency>
+
+		<dependency>
+			<groupId>org.scala-tools.sbinary</groupId>
+			<artifactId>sbinary_2.9.0</artifactId>
+			<version>0.4.0</version>
+		</dependency>
+        <!--  LVG added by dependency parser.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-lvg</artifactId>-->
+        <!--</dependency>-->
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-context-tokenizer</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-chunker</artifactId>
+		</dependency>
+        <!--  assertion does not depend upon ctakes-relation-extractor.  It uses relation types in:
+         JudgeAttributeInstances and MiPACQKnowtatorXMLReader -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-relation-extractor</artifactId>-->
+        <!--</dependency>-->
+		<dependency>
+			<groupId>org.cleartk</groupId>
+			<artifactId>cleartk-ml-liblinear</artifactId>
+		</dependency>
+	</dependencies>	 	
+	<build>
+		<plugins>
+				<plugin>
+				  <groupId>org.apache.uima</groupId>
+				  <artifactId>jcasgen-maven-plugin</artifactId>
+				  <version>2.9.0</version>				  
+				  <executions>
+				    <execution>
+				      <goals><goal>generate</goal></goals>
+				      <configuration>
+				        <typeSystemIncludes>
+                            <typeSystemInclude>src/main/resources/org/apache/ctakes/**/types/TypeSystem.xml
+                            </typeSystemInclude>
+				        </typeSystemIncludes>
+                          <limitToProject>true</limitToProject>
+				      </configuration>
+				    </execution>
+				    </executions>
+				</plugin>
+		</plugins>				
+ 	</build>	
+</project>

Modified: ctakes/trunk/ctakes-temporal/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/pom.xml?rev=1815709&r1=1815708&r2=1815709&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/pom.xml (original)
+++ ctakes/trunk/ctakes-temporal/pom.xml Sun Nov 19 08:00:56 2017
@@ -24,7 +24,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>ctakes-temporal</artifactId>
     <packaging>jar</packaging>
-    <name>Apache cTAKES Temporal Information Extraction</name>
+    <name>Apache cTAKES Temporal Information Extraction</name>	
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
@@ -79,7 +79,7 @@
 			<groupId>org.scala-lang</groupId>
 			<artifactId>scala-library</artifactId>
 			<version>2.11.7</version>
-		</dependency>
+		</dependency>		
 		<!--dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-sentdetect-cleartk</artifactId>

Modified: ctakes/trunk/ctakes-type-system/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-type-system/pom.xml?rev=1815709&r1=1815708&r2=1815709&view=diff
==============================================================================
--- ctakes/trunk/ctakes-type-system/pom.xml (original)
+++ ctakes/trunk/ctakes-type-system/pom.xml Sun Nov 19 08:00:56 2017
@@ -1,77 +1,81 @@
-<?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>
-	<artifactId>ctakes-type-system</artifactId>
-	<name>Apache cTAKES common type system</name>
-	<description>Defines the cTAKES type system UIMA annotation classes.</description>
-	<parent>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes</artifactId>
-		<version>4.0.1-SNAPSHOT</version>
-	</parent>
-	<dependencies>
-		<dependency>
-			<groupId>org.apache.uima</groupId>
-			<artifactId>uimaj-core</artifactId>
-		</dependency>
-		<!-- we excluded spring-context in the parent pom, include it here -->
-		<dependency>
-			<groupId>org.springframework</groupId>
-			<artifactId>spring-context</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>tw.edu.ntu.csie</groupId>
-			<artifactId>libsvm</artifactId>
-		</dependency>
-		<dependency>
-        	<groupId>junit</groupId>
-        	<artifactId>junit</artifactId>
-        <scope>test</scope>
-      </dependency>
-		<dependency>
-			<groupId>org.apache.uima</groupId>
-			<artifactId>uimafit-core</artifactId>
-		</dependency>
-	</dependencies>
-	<build>
-		<plugins>
-				<plugin>
-				  <groupId>org.apache.uima</groupId>
-				  <artifactId>jcasgen-maven-plugin</artifactId>
-				  <version>2.9.0</version>				  
-				  <executions>
-				    <execution>
-				      <goals><goal>generate</goal></goals>
-				      <configuration>
-				        <typeSystemIncludes>
-                            <typeSystemInclude>src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
-                            </typeSystemInclude>
-				        </typeSystemIncludes>
-                          <limitToProject>true</limitToProject>
-				      </configuration>
-				    </execution>
-				    </executions>
-				</plugin>
-		</plugins>				
- 	</build>
-</project>
+<?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>
+	<artifactId>ctakes-type-system</artifactId>
+	<name>Apache cTAKES common type system</name>
+	<description>Defines the cTAKES type system UIMA annotation classes.</description>	
+	<parent>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes</artifactId>
+		<version>4.0.1-SNAPSHOT</version>
+	</parent>
+	<dependencies>
+		<dependency>
+			<groupId>org.apache.uima</groupId>
+			<artifactId>uimaj-core</artifactId>
+		</dependency>
+		<!-- we excluded spring-context in the parent pom, include it here -->
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-context</artifactId>			
+		</dependency>
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-beans</artifactId>			
+		</dependency>
+		<dependency>
+			<groupId>tw.edu.ntu.csie</groupId>
+			<artifactId>libsvm</artifactId>
+		</dependency>
+		<dependency>
+        	<groupId>junit</groupId>
+        	<artifactId>junit</artifactId>
+        <scope>test</scope>
+      </dependency>
+		<dependency>
+			<groupId>org.apache.uima</groupId>
+			<artifactId>uimafit-core</artifactId>
+		</dependency>
+	</dependencies>
+	<build>
+		<plugins>
+				<plugin>
+				  <groupId>org.apache.uima</groupId>
+				  <artifactId>jcasgen-maven-plugin</artifactId>
+				  <version>2.9.0</version>				  
+				  <executions>
+				    <execution>
+				      <goals><goal>generate</goal></goals>
+				      <configuration>
+				        <typeSystemIncludes>
+                            <typeSystemInclude>src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
+                            </typeSystemInclude>
+				        </typeSystemIncludes>
+                          <limitToProject>true</limitToProject>
+				      </configuration>
+				    </execution>
+				    </executions>
+				</plugin>
+		</plugins>				
+ 	</build>
+</project>

Modified: ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/DBCollectionReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/DBCollectionReader.java?rev=1815709&r1=1815708&r2=1815709&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/DBCollectionReader.java (original)
+++ ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/DBCollectionReader.java Sun Nov 19 08:00:56 2017
@@ -36,7 +36,7 @@ import org.apache.uima.util.Progress;
 import org.apache.uima.util.ProgressImpl;
 import org.springframework.jdbc.core.RowCallbackHandler;
 import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate;
-import org.springframework.jdbc.core.simple.SimpleJdbcTemplate;
+import org.springframework.jdbc.core.JdbcTemplate;
 import org.springframework.jdbc.datasource.DataSourceTransactionManager;
 import org.springframework.jdbc.datasource.SimpleDriverDataSource;
 import org.springframework.jdbc.support.lob.DefaultLobHandler;
@@ -94,7 +94,7 @@ public class DBCollectionReader extends
 	protected String keyTypeName = "org.apache.ctakes.ytex.uima.types.DocKey";
 
 	protected DataSource dataSource;
-	protected SimpleJdbcTemplate simpleJdbcTemplate;
+	protected JdbcTemplate jdbcTemplate;	
 	protected NamedParameterJdbcTemplate namedJdbcTemplate;
 	protected TransactionTemplate txTemplate;
 	protected boolean keyNameToLowerCase = true;
@@ -162,8 +162,8 @@ public class DBCollectionReader extends
 			dataSource = (DataSource) ApplicationContextHolder
 					.getApplicationContext().getBean(
 							"collectionReaderDataSource");
-		}
-		simpleJdbcTemplate = new SimpleJdbcTemplate(dataSource);
+		}		
+		jdbcTemplate = new JdbcTemplate(dataSource);
 		namedJdbcTemplate = new NamedParameterJdbcTemplate(dataSource);
 	}
 
@@ -175,7 +175,7 @@ public class DBCollectionReader extends
 						@Override
 						public List<Map<String, Object>> doInTransaction(
 								TransactionStatus arg0) {
-							return simpleJdbcTemplate
+							return jdbcTemplate
 									.queryForList(queryGetDocumentKeys);
 						}
 					});

Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DBConsumerTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DBConsumerTest.java?rev=1815709&r1=1815708&r2=1815709&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DBConsumerTest.java (original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DBConsumerTest.java Sun Nov 19 08:00:56 2017
@@ -134,19 +134,19 @@ public class DBConsumerTest {
 		String query = String.format(
 				"select count(*) from %sdocument where instance_id=%s",
 				schemaPrefix, key);
-		Assert.assertTrue(query, jt.queryForInt(query) == 1);
+		Assert.assertTrue(query, jt.queryForObject(query,Integer.class) == 1);
 		query = String
 				.format("select count(*) from %sdocument d inner join %sanno_base ab on ab.document_id = d.document_id inner join %sanno_segment s on s.anno_base_id = ab.anno_base_id where d.instance_id=%s",
 						schemaPrefix, schemaPrefix, schemaPrefix, key);
-		Assert.assertTrue(query, jt.queryForInt(query) == 1);
+		Assert.assertTrue(query, jt.queryForObject(query,Integer.class) == 1);
 		query = String
 				.format("select count(*) from %sdocument d inner join %sanno_base ab on ab.document_id = d.document_id inner join %sanno_sentence s on s.anno_base_id = ab.anno_base_id where d.instance_id=%s",
 						schemaPrefix, schemaPrefix, schemaPrefix, key);
-		Assert.assertTrue(query, jt.queryForInt(query) > 1);
+		Assert.assertTrue(query, jt.queryForObject(query,Integer.class) > 1);
 		query = String
 				.format("select count(*) from %sdocument d inner join %sanno_base ab on ab.document_id = d.document_id inner join %sanno_token s on s.anno_base_id = ab.anno_base_id where d.instance_id=%s",
 						schemaPrefix, schemaPrefix, schemaPrefix, key);
-		Assert.assertTrue(query, jt.queryForInt(query) > 1);
+		Assert.assertTrue(query, jt.queryForObject(query,Integer.class) > 1);
 	}
 
 }

Modified: ctakes/trunk/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/ConceptSearchServiceImpl.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/ConceptSearchServiceImpl.java?rev=1815709&r1=1815708&r2=1815709&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/ConceptSearchServiceImpl.java (original)
+++ ctakes/trunk/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/ConceptSearchServiceImpl.java Sun Nov 19 08:00:56 2017
@@ -32,7 +32,7 @@ import javax.sql.DataSource;
 
 import org.springframework.beans.factory.InitializingBean;
 import org.springframework.jdbc.core.RowMapper;
-import org.springframework.jdbc.core.simple.SimpleJdbcTemplate;
+import org.springframework.jdbc.core.JdbcTemplate;
 
 public class ConceptSearchServiceImpl implements ConceptSearchService,
 		InitializingBean {
@@ -55,7 +55,7 @@ public class ConceptSearchServiceImpl im
 	private DataSource dataSource;
 	private String fwordToConceptIdQuery;
 
-	private SimpleJdbcTemplate jdbcTemplate;
+	private JdbcTemplate jdbcTemplate;
 
 	private Properties searchProperties;
 	private Properties ytexProperties;
@@ -156,8 +156,8 @@ public class ConceptSearchServiceImpl im
 	}
 
 	public void setDataSource(DataSource dataSource) {
-		this.dataSource = dataSource;
-		this.jdbcTemplate = new SimpleJdbcTemplate(dataSource);
+		this.dataSource = dataSource;		
+		this.jdbcTemplate = new JdbcTemplate(dataSource);
 	}
 
 	public void setSearchProperties(Properties searchProperties) {

Modified: ctakes/trunk/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/DocumentSearchServiceImpl.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/DocumentSearchServiceImpl.java?rev=1815709&r1=1815708&r2=1815709&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/DocumentSearchServiceImpl.java (original)
+++ ctakes/trunk/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/DocumentSearchServiceImpl.java Sun Nov 19 08:00:56 2017
@@ -33,7 +33,8 @@ import org.apache.commons.logging.LogFac
 import org.hibernate.SessionFactory;
 import org.springframework.beans.factory.InitializingBean;
 import org.springframework.jdbc.core.RowMapper;
-import org.springframework.jdbc.core.simple.SimpleJdbcTemplate;
+import org.springframework.jdbc.core.JdbcTemplate;
+
 
 public class DocumentSearchServiceImpl implements DocumentSearchService,
 		InitializingBean {
@@ -54,8 +55,8 @@ public class DocumentSearchServiceImpl i
 	}
 	private static final Log log = LogFactory
 			.getLog(DocumentSearchServiceImpl.class);
-	private DataSource dataSource;
-	private SimpleJdbcTemplate jdbcTemplate;
+	private DataSource dataSource;	
+	private JdbcTemplate jdbcTemplate;
 	private String query;
 
 	private Properties searchProperties;
@@ -185,8 +186,8 @@ public class DocumentSearchServiceImpl i
 	}
 
 	public void setDataSource(DataSource dataSource) {
-		this.dataSource = dataSource;
-		this.jdbcTemplate = new SimpleJdbcTemplate(dataSource);
+		this.dataSource = dataSource;		
+		this.jdbcTemplate = new JdbcTemplate(dataSource);
 	}
 
 	public void setSearchProperties(Properties searchProperties) {

Modified: ctakes/trunk/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/DocumentViewBean.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/DocumentViewBean.java?rev=1815709&r1=1815708&r2=1815709&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/DocumentViewBean.java (original)
+++ ctakes/trunk/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/DocumentViewBean.java Sun Nov 19 08:00:56 2017
@@ -25,7 +25,7 @@ import javax.faces.context.FacesContext;
 import javax.sql.DataSource;
 
 import org.apache.commons.lang.StringEscapeUtils;
-import org.springframework.jdbc.core.simple.SimpleJdbcTemplate;
+import org.springframework.jdbc.core.JdbcTemplate;
 
 /**
  * JSF bean for viewing a document retrieved via semanticSearch.jspx. Relies on
@@ -42,8 +42,8 @@ public class DocumentViewBean implements
 	private static final long serialVersionUID = 1L;
 	private transient DataSource dataSource;
 	private String docText;
-	private int documentID;
-	private transient SimpleJdbcTemplate jdbcTemplate;
+	private int documentID;	
+	private transient JdbcTemplate jdbcTemplate;
 	private String rawText;
 
 	private Properties searchProperties;
@@ -106,8 +106,8 @@ public class DocumentViewBean implements
 	}
 
 	public void setDataSource(DataSource dataSource) {
-		this.dataSource = dataSource;
-		this.jdbcTemplate = new SimpleJdbcTemplate(dataSource);
+		this.dataSource = dataSource;		
+		this.jdbcTemplate = new JdbcTemplate(dataSource);
 	}
 
 	public void setSearchProperties(Properties searchProperties) {

Modified: ctakes/trunk/ctakes-ytex/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/pom.xml?rev=1815709&r1=1815708&r2=1815709&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/pom.xml (original)
+++ ctakes/trunk/ctakes-ytex/pom.xml Sun Nov 19 08:00:56 2017
@@ -139,18 +139,19 @@
 		</dependency>
 		<dependency>
 			<groupId>org.springframework</groupId>
-			<artifactId>spring-jdbc</artifactId>
-			<version>3.1.2.RELEASE</version>
+			<artifactId>spring-jdbc</artifactId>			
 		</dependency>
 		<dependency>
 			<groupId>org.springframework</groupId>
-			<artifactId>spring-orm</artifactId>
-			<version>3.1.2.RELEASE</version>
+			<artifactId>spring-orm</artifactId>			
 		</dependency>
 		<dependency>
 			<groupId>org.springframework</groupId>
 			<artifactId>spring-aop</artifactId>
-			<version>3.1.2.RELEASE</version>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-context-support</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>org.aspectj</groupId>

Modified: ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/AbstractBagOfWordsExporter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/AbstractBagOfWordsExporter.java?rev=1815709&r1=1815708&r2=1815709&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/AbstractBagOfWordsExporter.java (original)
+++ ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/AbstractBagOfWordsExporter.java Sun Nov 19 08:00:56 2017
@@ -38,7 +38,6 @@ import javax.sql.DataSource;
 import org.springframework.jdbc.core.JdbcTemplate;
 import org.springframework.jdbc.core.PreparedStatementCreator;
 import org.springframework.jdbc.core.RowCallbackHandler;
-import org.springframework.jdbc.core.simple.SimpleJdbcTemplate;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallback;
@@ -46,7 +45,6 @@ import org.springframework.transaction.s
 
 public class AbstractBagOfWordsExporter {
 
-	protected SimpleJdbcTemplate simpleJdbcTemplate;
 	protected JdbcTemplate jdbcTemplate;
 	protected PlatformTransactionManager transactionManager;
 	protected TransactionTemplate txNew;
@@ -67,8 +65,7 @@ public class AbstractBagOfWordsExporter
 	}
 
 	public void setDataSource(DataSource ds) {
-		this.jdbcTemplate = new JdbcTemplate(ds);
-		this.simpleJdbcTemplate = new SimpleJdbcTemplate(ds);
+		this.jdbcTemplate = new JdbcTemplate(ds);		
 	}
 
 	public DataSource getDataSource(DataSource ds) {

Modified: ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SparseDataExporterImpl.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SparseDataExporterImpl.java?rev=1815709&r1=1815708&r2=1815709&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SparseDataExporterImpl.java (original)
+++ ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SparseDataExporterImpl.java Sun Nov 19 08:00:56 2017
@@ -44,7 +44,6 @@ import org.apache.commons.logging.LogFac
 import org.springframework.jdbc.core.JdbcTemplate;
 import org.springframework.jdbc.core.RowCallbackHandler;
 import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate;
-import org.springframework.jdbc.core.simple.SimpleJdbcTemplate;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallback;
 import org.springframework.transaction.support.TransactionTemplate;
@@ -98,9 +97,7 @@ public class SparseDataExporterImpl impl
 
 	protected NamedParameterJdbcTemplate namedJdbcTemplate;
 
-	protected Map<String, SparseDataFormatterFactory> nameToFormatterMap = new HashMap<String, SparseDataFormatterFactory>();
-
-	protected SimpleJdbcTemplate simpleJdbcTemplate;
+	protected Map<String, SparseDataFormatterFactory> nameToFormatterMap = new HashMap<String, SparseDataFormatterFactory>();	
 
 	protected TransactionTemplate txTemplateNew;
 
@@ -440,8 +437,7 @@ public class SparseDataExporterImpl impl
 	}
 
 	public void setDataSource(DataSource ds) {
-		this.jdbcTemplate = new JdbcTemplate(ds);
-		this.simpleJdbcTemplate = new SimpleJdbcTemplate(ds);
+		this.jdbcTemplate = new JdbcTemplate(ds);		
 		this.namedJdbcTemplate = new NamedParameterJdbcTemplate(ds);
 	}
 



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