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From chen...@apache.org
Subject svn commit: r1463641 [8/42] - in /ctakes/trunk: ctakes-assertion-res/ ctakes-assertion-res/.settings/ ctakes-assertion-res/src/ ctakes-assertion-res/src/main/ ctakes-assertion-res/src/main/resources/ ctakes-assertion-res/src/main/resources/org/ ctakes-...
Date Tue, 02 Apr 2013 17:44:41 GMT
Added: ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.jdt.core.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.jdt.core.prefs?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.jdt.core.prefs (added)
+++ ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.jdt.core.prefs Tue Apr  2 17:41:30 2013
@@ -0,0 +1,88 @@
+eclipse.preferences.version=1
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+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionExemptExceptionAndThrowable=enabled
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+org.eclipse.jdt.core.compiler.problem.unusedParameter=warning
+org.eclipse.jdt.core.compiler.problem.unusedParameterIncludeDocCommentReference=enabled
+org.eclipse.jdt.core.compiler.problem.unusedParameterWhenImplementingAbstract=disabled
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+org.eclipse.jdt.core.compiler.problem.unusedPrivateMember=warning
+org.eclipse.jdt.core.compiler.problem.unusedWarningToken=ignore
+org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning
+org.eclipse.jdt.core.compiler.source=1.6

Added: ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.ltk.core.refactoring.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.ltk.core.refactoring.prefs?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.ltk.core.refactoring.prefs (added)
+++ ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.ltk.core.refactoring.prefs Tue Apr  2 17:41:30 2013
@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+org.eclipse.ltk.core.refactoring.enable.project.refactoring.history=false

Added: ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.m2e.core.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.m2e.core.prefs?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.m2e.core.prefs (added)
+++ ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.m2e.core.prefs Tue Apr  2 17:41:30 2013
@@ -0,0 +1,4 @@
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

Added: ctakes/trunk/ctakes-constituency-parser-res/LICENSE
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser-res/LICENSE?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser-res/LICENSE (added)
+++ ctakes/trunk/ctakes-constituency-parser-res/LICENSE Tue Apr  2 17:41:30 2013
@@ -0,0 +1,202 @@
+
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Added: ctakes/trunk/ctakes-constituency-parser-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser-res/pom.xml?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser-res/pom.xml (added)
+++ ctakes/trunk/ctakes-constituency-parser-res/pom.xml Tue Apr  2 17:41:30 2013
@@ -0,0 +1,49 @@
+<?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>3.1.0-SNAPSHOT</version>
+  </parent>
+  <artifactId>ctakes-constituency-parser-res</artifactId>
+  <name>Apache cTAKES Resources constituency-parser</name>
+  <description>Resources Project for constituency-parser</description>
+  <dependencies>
+     <dependency>
+		<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-type-system</artifactId>
+	 </dependency>
+  </dependencies>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.cleartk</groupId>
+				<artifactId>jcasgen-maven-plugin</artifactId>
+				<configuration>
+					<typeSystem>src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml</typeSystem>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>  
+</project>
\ No newline at end of file

Added: ctakes/trunk/ctakes-constituency-parser-res/src/main/resources/org/apache/ctakes/constituency/parser/models/sharpacq-1.5.bin
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser-res/src/main/resources/org/apache/ctakes/constituency/parser/models/sharpacq-1.5.bin?rev=1463641&view=auto
==============================================================================
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    svn:mime-type = application/octet-stream

Added: ctakes/trunk/ctakes-constituency-parser-res/src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser-res/src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser-res/src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml (added)
+++ ctakes/trunk/ctakes-constituency-parser-res/src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml Tue Apr  2 17:41:30 2013
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
+  <name>org.apache.ctakes.constituency.parser.types.LabeledTree</name>
+  <description/>
+  <version>1.0</version>
+  <vendor/>
+  <types>
+    <typeDescription>
+      <name>org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree</name>
+      <description/>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+      <features>
+        <featureDescription>
+          <name>label</name>
+          <description/>
+          <rangeTypeName>uima.cas.Boolean</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>tree</name>
+          <description/>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+      </features>
+    </typeDescription>
+  </types>
+</typeSystemDescription>

Added: ctakes/trunk/ctakes-core-res/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core-res/.classpath?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core-res/.classpath (added)
+++ ctakes/trunk/ctakes-core-res/.classpath Tue Apr  2 17:41:30 2013
@@ -0,0 +1,31 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

Added: ctakes/trunk/ctakes-core-res/.project
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core-res/.project?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core-res/.project (added)
+++ ctakes/trunk/ctakes-core-res/.project Tue Apr  2 17:41:30 2013
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>ctakes-core-res</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+	</natures>
+</projectDescription>

Added: ctakes/trunk/ctakes-core-res/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core-res/.settings/org.eclipse.core.resources.prefs?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core-res/.settings/org.eclipse.core.resources.prefs (added)
+++ ctakes/trunk/ctakes-core-res/.settings/org.eclipse.core.resources.prefs Tue Apr  2 17:41:30 2013
@@ -0,0 +1,5 @@
+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding//src/main/resources=UTF-8
+encoding//src/test/java=UTF-8
+encoding/<project>=UTF-8

Added: ctakes/trunk/ctakes-core-res/.settings/org.eclipse.jdt.core.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core-res/.settings/org.eclipse.jdt.core.prefs?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core-res/.settings/org.eclipse.jdt.core.prefs (added)
+++ ctakes/trunk/ctakes-core-res/.settings/org.eclipse.jdt.core.prefs Tue Apr  2 17:41:30 2013
@@ -0,0 +1,88 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.annotation.missingNonNullByDefaultAnnotation=ignore
+org.eclipse.jdt.core.compiler.annotation.nonnull=org.eclipse.jdt.annotation.NonNull
+org.eclipse.jdt.core.compiler.annotation.nonnullbydefault=org.eclipse.jdt.annotation.NonNullByDefault
+org.eclipse.jdt.core.compiler.annotation.nullable=org.eclipse.jdt.annotation.Nullable
+org.eclipse.jdt.core.compiler.annotation.nullanalysis=disabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.problem.annotationSuperInterface=warning
+org.eclipse.jdt.core.compiler.problem.autoboxing=ignore
+org.eclipse.jdt.core.compiler.problem.comparingIdentical=warning
+org.eclipse.jdt.core.compiler.problem.deadCode=warning
+org.eclipse.jdt.core.compiler.problem.deprecation=warning
+org.eclipse.jdt.core.compiler.problem.deprecationInDeprecatedCode=disabled
+org.eclipse.jdt.core.compiler.problem.deprecationWhenOverridingDeprecatedMethod=disabled
+org.eclipse.jdt.core.compiler.problem.discouragedReference=warning
+org.eclipse.jdt.core.compiler.problem.emptyStatement=warning
+org.eclipse.jdt.core.compiler.problem.explicitlyClosedAutoCloseable=warning
+org.eclipse.jdt.core.compiler.problem.fallthroughCase=ignore
+org.eclipse.jdt.core.compiler.problem.fatalOptionalError=disabled
+org.eclipse.jdt.core.compiler.problem.fieldHiding=warning
+org.eclipse.jdt.core.compiler.problem.finalParameterBound=warning
+org.eclipse.jdt.core.compiler.problem.finallyBlockNotCompletingNormally=warning
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.problem.hiddenCatchBlock=warning
+org.eclipse.jdt.core.compiler.problem.includeNullInfoFromAsserts=disabled
+org.eclipse.jdt.core.compiler.problem.incompatibleNonInheritedInterfaceMethod=warning
+org.eclipse.jdt.core.compiler.problem.incompleteEnumSwitch=warning
+org.eclipse.jdt.core.compiler.problem.indirectStaticAccess=warning
+org.eclipse.jdt.core.compiler.problem.localVariableHiding=warning
+org.eclipse.jdt.core.compiler.problem.methodWithConstructorName=warning
+org.eclipse.jdt.core.compiler.problem.missingDefaultCase=ignore
+org.eclipse.jdt.core.compiler.problem.missingDeprecatedAnnotation=warning
+org.eclipse.jdt.core.compiler.problem.missingEnumCaseDespiteDefault=disabled
+org.eclipse.jdt.core.compiler.problem.missingHashCodeMethod=warning
+org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotation=warning
+org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotationForInterfaceMethodImplementation=disabled
+org.eclipse.jdt.core.compiler.problem.missingSerialVersion=warning
+org.eclipse.jdt.core.compiler.problem.missingSynchronizedOnInheritedMethod=warning
+org.eclipse.jdt.core.compiler.problem.noEffectAssignment=warning
+org.eclipse.jdt.core.compiler.problem.noImplicitStringConversion=warning
+org.eclipse.jdt.core.compiler.problem.nonExternalizedStringLiteral=ignore
+org.eclipse.jdt.core.compiler.problem.nullAnnotationInferenceConflict=error
+org.eclipse.jdt.core.compiler.problem.nullReference=warning
+org.eclipse.jdt.core.compiler.problem.nullSpecViolation=error
+org.eclipse.jdt.core.compiler.problem.nullUncheckedConversion=warning
+org.eclipse.jdt.core.compiler.problem.overridingPackageDefaultMethod=warning
+org.eclipse.jdt.core.compiler.problem.parameterAssignment=ignore
+org.eclipse.jdt.core.compiler.problem.possibleAccidentalBooleanAssignment=warning
+org.eclipse.jdt.core.compiler.problem.potentialNullReference=warning
+org.eclipse.jdt.core.compiler.problem.potentiallyUnclosedCloseable=warning
+org.eclipse.jdt.core.compiler.problem.rawTypeReference=warning
+org.eclipse.jdt.core.compiler.problem.redundantNullAnnotation=warning
+org.eclipse.jdt.core.compiler.problem.redundantNullCheck=warning
+org.eclipse.jdt.core.compiler.problem.redundantSpecificationOfTypeArguments=warning
+org.eclipse.jdt.core.compiler.problem.redundantSuperinterface=warning
+org.eclipse.jdt.core.compiler.problem.reportMethodCanBePotentiallyStatic=ignore
+org.eclipse.jdt.core.compiler.problem.reportMethodCanBeStatic=warning
+org.eclipse.jdt.core.compiler.problem.specialParameterHidingField=disabled
+org.eclipse.jdt.core.compiler.problem.staticAccessReceiver=warning
+org.eclipse.jdt.core.compiler.problem.suppressOptionalErrors=disabled
+org.eclipse.jdt.core.compiler.problem.suppressWarnings=enabled
+org.eclipse.jdt.core.compiler.problem.syntheticAccessEmulation=warning
+org.eclipse.jdt.core.compiler.problem.typeParameterHiding=warning
+org.eclipse.jdt.core.compiler.problem.unavoidableGenericTypeProblems=enabled
+org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
+org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
+org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unnecessaryElse=warning
+org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=warning
+org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownException=warning
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionExemptExceptionAndThrowable=enabled
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionIncludeDocCommentReference=enabled
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionWhenOverriding=disabled
+org.eclipse.jdt.core.compiler.problem.unusedImport=warning
+org.eclipse.jdt.core.compiler.problem.unusedLabel=warning
+org.eclipse.jdt.core.compiler.problem.unusedLocal=warning
+org.eclipse.jdt.core.compiler.problem.unusedObjectAllocation=warning
+org.eclipse.jdt.core.compiler.problem.unusedParameter=warning
+org.eclipse.jdt.core.compiler.problem.unusedParameterIncludeDocCommentReference=enabled
+org.eclipse.jdt.core.compiler.problem.unusedParameterWhenImplementingAbstract=disabled
+org.eclipse.jdt.core.compiler.problem.unusedParameterWhenOverridingConcrete=disabled
+org.eclipse.jdt.core.compiler.problem.unusedPrivateMember=warning
+org.eclipse.jdt.core.compiler.problem.unusedWarningToken=ignore
+org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning
+org.eclipse.jdt.core.compiler.source=1.6

Added: ctakes/trunk/ctakes-core-res/.settings/org.eclipse.ltk.core.refactoring.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core-res/.settings/org.eclipse.ltk.core.refactoring.prefs?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core-res/.settings/org.eclipse.ltk.core.refactoring.prefs (added)
+++ ctakes/trunk/ctakes-core-res/.settings/org.eclipse.ltk.core.refactoring.prefs Tue Apr  2 17:41:30 2013
@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+org.eclipse.ltk.core.refactoring.enable.project.refactoring.history=false

Added: ctakes/trunk/ctakes-core-res/.settings/org.eclipse.m2e.core.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core-res/.settings/org.eclipse.m2e.core.prefs?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core-res/.settings/org.eclipse.m2e.core.prefs (added)
+++ ctakes/trunk/ctakes-core-res/.settings/org.eclipse.m2e.core.prefs Tue Apr  2 17:41:30 2013
@@ -0,0 +1,4 @@
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

Added: ctakes/trunk/ctakes-core-res/LICENSE
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core-res/LICENSE?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core-res/LICENSE (added)
+++ ctakes/trunk/ctakes-core-res/LICENSE Tue Apr  2 17:41:30 2013
@@ -0,0 +1,202 @@
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
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+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
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+
+   6. Trademarks. This License does not grant permission to use the trade
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+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
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+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
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+
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+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
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+      file or class name and description of purpose be included on the
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+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
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+   See the License for the specific language governing permissions and
+   limitations under the License.

Added: ctakes/trunk/ctakes-core-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core-res/pom.xml?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core-res/pom.xml (added)
+++ ctakes/trunk/ctakes-core-res/pom.xml Tue Apr  2 17:41:30 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>3.1.0-SNAPSHOT</version>
+  </parent>
+  <artifactId>ctakes-core-res</artifactId>
+  <name>Apache cTAKES Resources core</name>
+  <description>Resources Project for ctakes-core</description>
+</project>
\ No newline at end of file

Added: ctakes/trunk/ctakes-core-res/src/main/resources/log4j.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core-res/src/main/resources/log4j.xml?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core-res/src/main/resources/log4j.xml (added)
+++ ctakes/trunk/ctakes-core-res/src/main/resources/log4j.xml Tue Apr  2 17:41:30 2013
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8" ?> <!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
+<log4j:configuration debug="true"
+	xmlns:log4j='http://jakarta.apache.org/log4j/'>
+	<appender name="consoleAppender" class="org.apache.log4j.ConsoleAppender">
+		<layout class="org.apache.log4j.PatternLayout">
+			<param name="ConversionPattern" value="%d{dd MMM yyyy HH:mm:ss} %5p %c{1} - %m%n" />
+		</layout>
+	</appender>
+	<appender name="fileAppender" class="org.apache.log4j.RollingFileAppender">
+		<param name="append" value="false" />
+		<param name="file" value="out/ctakes.log" />
+		<layout class="org.apache.log4j.PatternLayout">
+			<param name="ConversionPattern" value="%d{ABSOLUTE} %-5p [%c{1}] %m%n" />
+		</layout>
+	</appender>
+	<root>
+		<level value="INFO" />
+		<appender-ref ref="consoleAppender" />
+		<!--  <appender-ref ref="fileAppender" /> -->
+	</root>
+</log4j:configuration> 
\ No newline at end of file

Added: ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/analysis_engine/SentenceDetectorAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/analysis_engine/SentenceDetectorAnnotator.xml?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/analysis_engine/SentenceDetectorAnnotator.xml (added)
+++ ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/analysis_engine/SentenceDetectorAnnotator.xml Tue Apr  2 17:41:30 2013
@@ -0,0 +1,93 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+<primitive>true</primitive>
+<annotatorImplementationName>org.apache.ctakes.core.ae.SentenceDetector</annotatorImplementationName>
+<analysisEngineMetaData>
+<name>Sentence Detector annotator</name>
+<description>Discovers sentence boundaries.</description>
+<version>2.1</version>
+<vendor>Mayo Clinic</vendor>
+<configurationParameters>
+<configurationParameter>
+<name>SegmentsToSkip</name>
+<type>String</type>
+<multiValued>true</multiValued>
+<mandatory>false</mandatory>
+</configurationParameter>
+</configurationParameters>
+<configurationParameterSettings>
+<nameValuePair>
+<name>SegmentsToSkip</name>
+<value>
+<array/>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+<typeSystemDescription/>
+<typePriorities/>
+<fsIndexCollection/>
+<capabilities>
+<capability>
+<inputs>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+</inputs>
+<outputs>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+</outputs>
+<languagesSupported/>
+</capability>
+</capabilities>
+<operationalProperties>
+<modifiesCas>true</modifiesCas>
+<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+<outputsNewCASes>false</outputsNewCASes>
+</operationalProperties>
+</analysisEngineMetaData>
+<externalResourceDependencies>
+<externalResourceDependency>
+<key>MaxentModel</key>
+<description></description>
+<interfaceName>org.apache.ctakes.core.resource.MaxentModelResource</interfaceName>
+<optional>false</optional>
+</externalResourceDependency>
+</externalResourceDependencies>
+<resourceManagerConfiguration>
+<externalResources>
+<externalResource>
+<name>MaxentModelFile</name>
+<description></description>
+<fileResourceSpecifier>
+<fileUrl>file:org/apache/ctakes/core/sentdetect/sdmed.mod</fileUrl>
+</fileResourceSpecifier>
+<implementationName>org.apache.ctakes.core.resource.SuffixMaxentModelResourceImpl</implementationName>
+</externalResource>
+</externalResources>
+<externalResourceBindings>
+<externalResourceBinding>
+<key>MaxentModel</key>
+<resourceName>MaxentModelFile</resourceName>
+</externalResourceBinding>
+</externalResourceBindings>
+</resourceManagerConfiguration>
+</taeDescription>

Added: ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/analysis_engine/TokenizerAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/analysis_engine/TokenizerAnnotator.xml?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/analysis_engine/TokenizerAnnotator.xml (added)
+++ ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/analysis_engine/TokenizerAnnotator.xml Tue Apr  2 17:41:30 2013
@@ -0,0 +1,76 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+<primitive>true</primitive>
+<annotatorImplementationName>org.apache.ctakes.core.ae.TokenizerAnnotatorPTB</annotatorImplementationName>
+<analysisEngineMetaData>
+<name>TokenizerAnnotatorPTB</name>
+<description>Discovers tokens in the given text, following Penn TreeBank tokenization rules.  These tokens consist of words, punctuation, etc...</description>
+<version>2.3</version>
+<vendor>Mayo Clinic</vendor>
+<configurationParameters>
+<configurationParameter>
+<name>SegmentsToSkip</name>
+<description>Segments to skip.</description>
+<type>String</type>
+<multiValued>true</multiValued>
+<mandatory>false</mandatory>
+</configurationParameter>
+</configurationParameters>
+<configurationParameterSettings>
+<nameValuePair>
+<name>SegmentsToSkip</name>
+<value>
+<array/>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+<typeSystemDescription>
+<imports>
+<import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
+</imports>
+</typeSystemDescription>
+<typePriorities/>
+<fsIndexCollection/>
+<capabilities>
+<capability>
+<inputs>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Segment</type>
+</inputs>
+<outputs>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+</outputs>
+<languagesSupported/>
+</capability>
+</capabilities>
+<operationalProperties>
+<modifiesCas>true</modifiesCas>
+<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+<outputsNewCASes>false</outputsNewCASes>
+</operationalProperties>
+</analysisEngineMetaData>
+<externalResourceDependencies>
+</externalResourceDependencies>
+<resourceManagerConfiguration>
+</resourceManagerConfiguration>
+</taeDescription>

Added: ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/cc/jdbc/TestBinding.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/cc/jdbc/TestBinding.xml?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/cc/jdbc/TestBinding.xml (added)
+++ ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/cc/jdbc/TestBinding.xml Tue Apr  2 17:41:30 2013
@@ -0,0 +1,58 @@
+<?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.
+
+-->
+<root>
+	<preparedStatements>
+		<preparedStatement id="TEST_QUERY_PREP_STMT" sql="select count(*) as MYCOUNT from TXTPH3.JDBC_CC_TEST"/>
+		<preparedStatement id="TEST_INSERT_PREP_STMT" sql="insert into TXTPH3.JDBC_CC_TEST (C1, C2, C3,C4) values (?,?,?,?)"/>
+	</preparedStatements>
+	<executionFlow>
+		<query idref="TEST_QUERY_PREP_STMT">
+			<paramBindings/>
+			<resultSetBindings>
+				<binding>
+					<variable id="MYCOUNT" scope="GLOBAL"/>
+					<prepStmtResult column="MYCOUNT" dataType="INTEGER"/>
+				</binding>
+			</resultSetBindings>
+		</query>
+		<insert idref="TEST_INSERT_PREP_STMT" batchUpdate="TRUE">
+			<paramBindings>
+				<binding>
+					<prepStmtParam dataType="DECIMAL"/>
+					<variableRef idref="MYCOUNT" scope="GLOBAL"/>
+				</binding>
+				<binding>
+					<prepStmtParam dataType="INTEGER"/>
+					<variableRef idref="MYCOUNT" scope="GLOBAL"/>
+				</binding>
+				<binding>
+					<prepStmtParam dataType="CLOB"/>
+					<variableRef idref="NORM_DOC_TEXT" scope="GLOBAL"/>
+				</binding>
+				<binding>
+					<prepStmtParam dataType="BLOB"/>
+					<variableRef idref="NORM_DOC_MAP" scope="GLOBAL"/>
+				</binding>
+			</paramBindings>
+		</insert>
+	</executionFlow>
+</root>

Added: ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/eclipse/spellingdictionaryforsourcecode.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/eclipse/spellingdictionaryforsourcecode.txt?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/eclipse/spellingdictionaryforsourcecode.txt (added)
+++ ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/eclipse/spellingdictionaryforsourcecode.txt Tue Apr  2 17:41:30 2013
@@ -0,0 +1,27 @@
+annotator
+tagger
+Treebank
+Penn
+config
+hsqldb
+jdbc
+download
+lvg
+edu
+mayo
+Mayo
+bmi
+uima
+UIMA
+apache
+Lvg
+xml
+org
+apache
+tcas
+jcas
+tgz
+chunker
+Chunker
+opennlp
+

Added: ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/log4j.properties
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/log4j.properties?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/log4j.properties (added)
+++ ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/log4j.properties Tue Apr  2 17:41:30 2013
@@ -0,0 +1,41 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
+###############################################################################
+
+log4j.rootLogger=INFO, Console
+
+###############################################################################
+
+# Rolling File Appender definition
+log4j.appender.RFile=org.apache.log4j.RollingFileAppender
+log4j.appender.RFile.File=textAnalysis.log
+log4j.appender.RFile.MaxFileSize=1024KB
+log4j.appender.RFile.MaxBackupIndex=1
+log4j.appender.RFile.layout=org.apache.log4j.PatternLayout
+log4j.appender.RFile.layout.ConversionPattern=%d %-5p %c %x - %m%n
+
+###############################################################################
+
+# Console Appender definition
+log4j.appender.Console=org.apache.log4j.ConsoleAppender
+log4j.appender.Console.layout=org.apache.log4j.PatternLayout
+log4j.appender.Console.layout.ConversionPattern=%d %-5p %c %x - %m%n
+
+###############################################################################
\ No newline at end of file

Added: ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/sentdetect/README
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/sentdetect/README?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/sentdetect/README (added)
+++ ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/sentdetect/README Tue Apr  2 17:41:30 2013
@@ -0,0 +1,110 @@
+Contents:
+- Included sentence detector model 
+- Training a sentence detector model from the included sample data  
+- Training a sentence detector model from other training data  
+- Verifying you can train a sentence detector model successfully          
+- FYI - Using opennlp directly
+- Running the SentenceDetectorAnnotator analysis engine
+	- SentenceDetectorAggregate.xml
+	- SentenceDetectorCPE.xml
+	- SentenceDetectorAnnotator.xml
+
+
+################################################################
+Included sentence detector model  
+################################################################
+A sentence detector model is included with this project.
+
+The model derives from a combination of GENIA, Penn Treebank (Wall Street Journal) and anonymized
+clinical data per Safe Harbor HIPAA guidelines. Prior to model building, the clinical data was 
+deidentified for patient names to preserve patient confidentiality. Any person name in the model 
+will originate from non-patient data sources.
+
+
+################################################################
+Training a sentence detector model from the included sample data  
+################################################################
+   
+To train a sentence detector that recognizes the same set of candidate
+end-of-sentence characters that the SentenceDetectorAnnotator uses, 
+using the included sample training sentences, use the included launch 
+called "SentenceDetector - train a new model", or use:
+  java org.apache.ctakes.core.ae.SentenceDetector 
+        data/test/sample_sd_training_sentences.txt 
+        resources/sentdetect/sample_sd.mod
+        
+
+###########################################################
+Training a sentence detector model from other training data 
+###########################################################
+
+To train a sentence detector that recognizes the same set of candidate
+end-of-sentence characters that the SentenceDetectorAnnotator uses, 
+on the Run dialog within eclipse, set the Program arguments on the Arguments 
+tab (the first argument is your sentences training data file) for the 
+included launch called "SentenceDetector - train a new model".
+
+The first argument is your sentences training data file
+The second argument is the name of the model file to be created
+The third argument is the number of iterations for training
+The fourth argument is the cutoff value used
+
+An alternative to using the launch is to use:
+  java org.apache.ctakes.core.ae.SentenceDetector sents_file model iters? cut?
+where sents_file contains one sentence per line,
+model is the file that is to be created, 
+and iters and cut are optional parameters.
+
+For example, sents_file could contain the following four lines:
+The boy ran.
+Did the girl run too?
+Yes, she did.
+Where did she go?
+
+
+##############################################################
+Verifying you can train a sentence detector model successfully          
+##############################################################
+
+Train a sentence detector model from the included sample data, as described 
+above.
+Compare the contents of your sentence detector model to the included sample
+sentence detector model.  You might use diff, like this:
+diff  resources/sentdetect/sample_sd.mod   resources/sentdetect/sample_sd_included.mod
+
+        
+############################
+FYI - Using opennlp directly
+############################
+ 
+You can train a sentence detector directly using the opennlp sentence detector 
+(SentenceDetectorME) with the default set of candidate end-of-sentence 
+characters, using 
+  java opennlp.tools.sentdetect.SentenceDetectorME infile outfile (iters cut)?
+where infile contains one sentence per line (new lines separating sentences)  
+For example, infile could contain the following four lines:
+The boy ran.
+Did the girl run too?
+Yes, she did.
+Where did she go?
+
+
+######################################################
+Running the SentenceDetectorAnnotator analysis engine
+######################################################
+
+Launch the "SentenceDetector annotator" run configuration.
+Open CPE SentenceDetectorCPE.xml, which uses the analysis
+engines listed in SentenceDetectorAggregate.xml.
+
+The aggregate analysis engine is defined to read from plain text file(s) in 
+data\test\sample_notes_plaintext
+using the FilesInDirectoryCollectionReader.
+
+Since the sentence annotator processes the text one section at a time, there 
+must be at least one section (segment) annotation for the SentenceDetectorAnnotator
+to add Sentence annotations. 
+Therefore the first analysis engine is the SimpleSegmentAnnotator, which
+creates a single Segment annotation that covers the entire text.
+Then the SentenceDetectorAnnotator analysis engine adds Sentence annotations.
+



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