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From mattco...@apache.org
Subject svn commit: r1425006 [1/3] - in /incubator/ctakes/trunk/ctakes-assertion-zoner: ./ .settings/ desc/ desc/cpe/ metadata/ src/ src/main/ src/main/java/ src/main/java/org/ src/main/java/org/mitre/ src/main/java/org/mitre/medfacts/ src/main/java/org/mitre/...
Date Fri, 21 Dec 2012 16:30:49 GMT
Author: mattcoarr
Date: Fri Dec 21 16:30:48 2012
New Revision: 1425006

URL: http://svn.apache.org/viewvc?rev=1425006&view=rev
Log:
adding the ctakes-assertion's zoner component (this is the assertion module's version of a sectionizer)

Added:
    incubator/ctakes/trunk/ctakes-assertion-zoner/
    incubator/ctakes/trunk/ctakes-assertion-zoner/.classpath
    incubator/ctakes/trunk/ctakes-assertion-zoner/.project
    incubator/ctakes/trunk/ctakes-assertion-zoner/.settings/
    incubator/ctakes/trunk/ctakes-assertion-zoner/.settings/org.eclipse.core.resources.prefs
    incubator/ctakes/trunk/ctakes-assertion-zoner/.settings/org.eclipse.jdt.core.prefs   (with props)
    incubator/ctakes/trunk/ctakes-assertion-zoner/.settings/org.eclipse.m2e.core.prefs
    incubator/ctakes/trunk/ctakes-assertion-zoner/desc/
    incubator/ctakes/trunk/ctakes-assertion-zoner/desc/ZonerDescriptor.xml   (with props)
    incubator/ctakes/trunk/ctakes-assertion-zoner/desc/ZonerDescriptorStyleMap.xml   (with props)
    incubator/ctakes/trunk/ctakes-assertion-zoner/desc/cpe/
    incubator/ctakes/trunk/ctakes-assertion-zoner/desc/cpe/zonermeds4.xml   (with props)
    incubator/ctakes/trunk/ctakes-assertion-zoner/metadata/
    incubator/ctakes/trunk/ctakes-assertion-zoner/metadata/install.xml   (with props)
    incubator/ctakes/trunk/ctakes-assertion-zoner/pom.xml
    incubator/ctakes/trunk/ctakes-assertion-zoner/pom.xml.backup01
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/java/
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/RunZoner.java
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/ZoneAnnotator.java   (with props)
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/META-INF/
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/META-INF/org.uimafit/
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/META-INF/org.uimafit/types.txt
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/types/
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/mitre/
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/mitre/medfacts/
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/mitre/medfacts/uima/
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/mitre/medfacts/uima/section_regex.04162012.xml   (with props)
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/mitre/medfacts/uima/section_regex.06162011.xml   (with props)
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/mitre/medfacts/uima/section_regex.out.xml   (with props)
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/mitre/medfacts/uima/section_regex.xml   (with props)
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/mitre/medfacts/uima/section_regex.xml.bak   (with props)
    incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/mitre/medfacts/uima/section_regex.xml.bak2   (with props)

Added: incubator/ctakes/trunk/ctakes-assertion-zoner/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion-zoner/.classpath?rev=1425006&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion-zoner/.classpath (added)
+++ incubator/ctakes/trunk/ctakes-assertion-zoner/.classpath Fri Dec 21 16:30:48 2012
@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<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/classes" path="target/generated-sources/jcasgen">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<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/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: incubator/ctakes/trunk/ctakes-assertion-zoner/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion-zoner/.project?rev=1425006&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion-zoner/.project (added)
+++ incubator/ctakes/trunk/ctakes-assertion-zoner/.project Fri Dec 21 16:30:48 2012
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>UIMA AFEM Zone Annotator</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.m2e.core.maven2Nature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.apache.uima.pear.UimaNature</nature>
+	</natures>
+</projectDescription>

Added: incubator/ctakes/trunk/ctakes-assertion-zoner/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion-zoner/.settings/org.eclipse.core.resources.prefs?rev=1425006&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion-zoner/.settings/org.eclipse.core.resources.prefs (added)
+++ incubator/ctakes/trunk/ctakes-assertion-zoner/.settings/org.eclipse.core.resources.prefs Fri Dec 21 16:30:48 2012
@@ -0,0 +1,5 @@
+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding//src/main/resources=UTF-8
+encoding//target/generated-sources/jcasgen=UTF-8
+encoding/<project>=UTF-8

Added: incubator/ctakes/trunk/ctakes-assertion-zoner/.settings/org.eclipse.jdt.core.prefs
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion-zoner/.settings/org.eclipse.jdt.core.prefs?rev=1425006&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion-zoner/.settings/org.eclipse.jdt.core.prefs (added)
+++ incubator/ctakes/trunk/ctakes-assertion-zoner/.settings/org.eclipse.jdt.core.prefs Fri Dec 21 16:30:48 2012
@@ -0,0 +1,12 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.6

Propchange: incubator/ctakes/trunk/ctakes-assertion-zoner/.settings/org.eclipse.jdt.core.prefs
------------------------------------------------------------------------------
    svn:executable = *

Added: incubator/ctakes/trunk/ctakes-assertion-zoner/.settings/org.eclipse.m2e.core.prefs
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion-zoner/.settings/org.eclipse.m2e.core.prefs?rev=1425006&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion-zoner/.settings/org.eclipse.m2e.core.prefs (added)
+++ incubator/ctakes/trunk/ctakes-assertion-zoner/.settings/org.eclipse.m2e.core.prefs Fri Dec 21 16:30:48 2012
@@ -0,0 +1,4 @@
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

Added: incubator/ctakes/trunk/ctakes-assertion-zoner/desc/ZonerDescriptor.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion-zoner/desc/ZonerDescriptor.xml?rev=1425006&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion-zoner/desc/ZonerDescriptor.xml (added)
+++ incubator/ctakes/trunk/ctakes-assertion-zoner/desc/ZonerDescriptor.xml Fri Dec 21 16:30:48 2012
@@ -0,0 +1,92 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+  <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+  <primitive>true</primitive>
+  <annotatorImplementationName>org.mitre.medfacts.uima.Zoner</annotatorImplementationName>
+  <analysisEngineMetaData>
+    <name>ZonerDescriptor</name>
+    <description/>
+    <version>1.0</version>
+    <vendor>MITRE</vendor>
+    <configurationParameters/>
+    <configurationParameterSettings/>
+    <typeSystemDescription>
+      <types>
+        <typeDescription>
+          <name>org.mitre.medfacts.uima.Heading</name>
+          <description>a section heading</description>
+          <supertypeName>uima.tcas.Annotation</supertypeName>
+          <features>
+            <featureDescription>
+              <name>label</name>
+              <description/>
+              <rangeTypeName>uima.cas.String</rangeTypeName>
+            </featureDescription>
+          </features>
+        </typeDescription>
+        <typeDescription>
+          <name>org.mitre.medfacts.uima.Zone</name>
+          <description>A document Zone, including its heading</description>
+          <supertypeName>uima.tcas.Annotation</supertypeName>
+          <features>
+            <featureDescription>
+              <name>label</name>
+              <description/>
+              <rangeTypeName>uima.cas.String</rangeTypeName>
+            </featureDescription>
+          </features>
+        </typeDescription>
+        <typeDescription>
+          <name>org.mitre.medfacts.uima.Subzone</name>
+          <description/>
+          <supertypeName>uima.tcas.Annotation</supertypeName>
+          <features>
+            <featureDescription>
+              <name>label</name>
+              <description/>
+              <rangeTypeName>uima.cas.String</rangeTypeName>
+            </featureDescription>
+          </features>
+        </typeDescription>
+      </types>
+    </typeSystemDescription>
+    <typePriorities/>
+    <fsIndexCollection/>
+    <capabilities>
+      <capability>
+        <inputs/>
+        <outputs/>
+        <languagesSupported/>
+      </capability>
+    </capabilities>
+    <operationalProperties>
+      <modifiesCas>true</modifiesCas>
+      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+      <outputsNewCASes>false</outputsNewCASes>
+    </operationalProperties>
+  </analysisEngineMetaData>
+  <externalResourceDependencies>
+    <externalResourceDependency>
+      <key>SectionRegex</key>
+      <description/>
+      <optional>false</optional>
+    </externalResourceDependency>
+  </externalResourceDependencies>
+  <resourceManagerConfiguration>
+    <externalResources>
+      <externalResource>
+        <name>SectionHeaderRegularExpressions</name>
+        <description/>
+        <fileResourceSpecifier>
+          <fileUrl>file:org/mitre/medfacts/uima/section_regex.xml</fileUrl>
+        </fileResourceSpecifier>
+      </externalResource>
+    </externalResources>
+    <externalResourceBindings>
+      <externalResourceBinding>
+        <key>SectionRegex</key>
+        <resourceName>SectionHeaderRegularExpressions</resourceName>
+      </externalResourceBinding>
+    </externalResourceBindings>
+  </resourceManagerConfiguration>
+</analysisEngineDescription>

Propchange: incubator/ctakes/trunk/ctakes-assertion-zoner/desc/ZonerDescriptor.xml
------------------------------------------------------------------------------
    svn:executable = *

Added: incubator/ctakes/trunk/ctakes-assertion-zoner/desc/ZonerDescriptorStyleMap.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion-zoner/desc/ZonerDescriptorStyleMap.xml?rev=1425006&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion-zoner/desc/ZonerDescriptorStyleMap.xml (added)
+++ incubator/ctakes/trunk/ctakes-assertion-zoner/desc/ZonerDescriptorStyleMap.xml Fri Dec 21 16:30:48 2012
@@ -0,0 +1,3 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<styleMap>
+</styleMap>

Propchange: incubator/ctakes/trunk/ctakes-assertion-zoner/desc/ZonerDescriptorStyleMap.xml
------------------------------------------------------------------------------
    svn:executable = *

Added: incubator/ctakes/trunk/ctakes-assertion-zoner/desc/cpe/zonermeds4.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion-zoner/desc/cpe/zonermeds4.xml?rev=1425006&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion-zoner/desc/cpe/zonermeds4.xml (added)
+++ incubator/ctakes/trunk/ctakes-assertion-zoner/desc/cpe/zonermeds4.xml Fri Dec 21 16:30:48 2012
@@ -0,0 +1,58 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<cpeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+    <collectionReader>
+        <collectionIterator>
+            <descriptor>
+                <import location="../../../../../../../apache-uima/examples/descriptors/collection_reader/FileSystemCollectionReader.xml"/>
+            </descriptor>
+            <configurationParameterSettings>
+                <nameValuePair>
+                    <name>InputDirectory</name>
+                    <value>
+                        <string>C:\a_projects\AFEM\i2b2 data\2009_Medications\TrainingDataText\4</string>
+                    </value>
+                </nameValuePair>
+            </configurationParameterSettings>
+        </collectionIterator>
+    </collectionReader>
+    <casProcessors casPoolSize="3" processingUnitThreadCount="1">
+        <casProcessor deployment="integrated" name="ZonerDescriptor">
+            <descriptor>
+                <import location="../ZonerDescriptor.xml"/>
+            </descriptor>
+            <deploymentParameters/>
+            <errorHandling>
+                <errorRateThreshold action="terminate" value="0/1000"/>
+                <maxConsecutiveRestarts action="terminate" value="30"/>
+                <timeout max="100000" default="-1"/>
+            </errorHandling>
+            <checkpoint batch="10000" time="1000ms"/>
+        </casProcessor>
+        <casProcessor deployment="integrated" name="Xmi Writer CAS Consumer">
+            <descriptor>
+                <import location="../../../../../../../apache-uima/examples/descriptors/cas_consumer/XmiWriterCasConsumer.xml"/>
+            </descriptor>
+            <deploymentParameters/>
+            <errorHandling>
+                <errorRateThreshold action="terminate" value="0/1000"/>
+                <maxConsecutiveRestarts action="terminate" value="30"/>
+                <timeout max="100000" default="-1"/>
+            </errorHandling>
+            <checkpoint batch="10000" time="1000ms"/>
+            <configurationParameterSettings>
+                <nameValuePair>
+                    <name>OutputDirectory</name>
+                    <value>
+                        <string>C:\a_projects\AFEM\i2b2 data\uimaout\Meds4</string>
+                    </value>
+                </nameValuePair>
+            </configurationParameterSettings>
+        </casProcessor>
+    </casProcessors>
+    <cpeConfig>
+        <numToProcess>-1</numToProcess>
+        <deployAs>immediate</deployAs>
+        <checkpoint batch="0" time="300000ms"/>
+        <timerImpl/>
+    </cpeConfig>
+</cpeDescription>

Propchange: incubator/ctakes/trunk/ctakes-assertion-zoner/desc/cpe/zonermeds4.xml
------------------------------------------------------------------------------
    svn:executable = *

Added: incubator/ctakes/trunk/ctakes-assertion-zoner/metadata/install.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion-zoner/metadata/install.xml?rev=1425006&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion-zoner/metadata/install.xml (added)
+++ incubator/ctakes/trunk/ctakes-assertion-zoner/metadata/install.xml Fri Dec 21 16:30:48 2012
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<COMPONENT_INSTALLATION_DESCRIPTOR>
+	<OS>
+		<NAME>Windows</NAME>
+	</OS>
+	<TOOLKITS>
+		<JDK_VERSION>1.4.0</JDK_VERSION>
+	</TOOLKITS>
+	<UIMA_FRAMEWORK>
+	</UIMA_FRAMEWORK>
+	<SUBMITTED_COMPONENT>
+		<ID>UIMA_AFEM_Zone_Annotator</ID>
+		<NAME></NAME>
+		<DESC>$main_root/desc/ZonerDescriptor.xml</DESC>
+		<DEPLOYMENT>standard</DEPLOYMENT>
+	</SUBMITTED_COMPONENT>
+	<INSTALLATION>
+		<PROCESS>
+			<ACTION>set_env_variable</ACTION>
+			<PARAMETERS>
+				<COMMENTS></COMMENTS>
+				<VAR_VALUE>$main_root/bin;$main_root/resources;$main_root/lib/med-facts-zoner-1.0-SNAPSHOT.jar;</VAR_VALUE>
+				<VAR_NAME>CLASSPATH</VAR_NAME>
+			</PARAMETERS>
+		</PROCESS>
+	</INSTALLATION>
+</COMPONENT_INSTALLATION_DESCRIPTOR>

Propchange: incubator/ctakes/trunk/ctakes-assertion-zoner/metadata/install.xml
------------------------------------------------------------------------------
    svn:executable = *

Added: incubator/ctakes/trunk/ctakes-assertion-zoner/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion-zoner/pom.xml?rev=1425006&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion-zoner/pom.xml (added)
+++ incubator/ctakes/trunk/ctakes-assertion-zoner/pom.xml Fri Dec 21 16:30:48 2012
@@ -0,0 +1,64 @@
+<?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-zoner</artifactId>
+	<name>Apache cTAKES Assertion's zoner</name>
+	<parent>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes</artifactId>
+		<version>3.1.0-incubating-SNAPSHOT</version>
+	</parent>
+
+
+	<dependencies>
+		<dependency>
+			<groupId>net.sf.mastif</groupId>
+			<artifactId>mastif-zoner</artifactId>
+			<version>1.5-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+      <groupId>org.apache.uima</groupId>
+      <artifactId>uimaj-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.uimafit</groupId>
+			<artifactId>uimafit</artifactId>
+		</dependency>
+    <dependency>
+      <groupId>org.apache.ctakes</groupId>
+      <artifactId>ctakes-core</artifactId>
+    </dependency>
+
+	</dependencies>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.cleartk</groupId>
+				<artifactId>jcasgen-maven-plugin</artifactId>
+				<configuration>
+					<typeSystem>src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml</typeSystem>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>
+</project>

Added: incubator/ctakes/trunk/ctakes-assertion-zoner/pom.xml.backup01
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion-zoner/pom.xml.backup01?rev=1425006&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion-zoner/pom.xml.backup01 (added)
+++ incubator/ctakes/trunk/ctakes-assertion-zoner/pom.xml.backup01 Fri Dec 21 16:30:48 2012
@@ -0,0 +1,251 @@
+<?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-zoner</artifactId>
+	<name>Apache cTAKES Assertion</name>
+	<parent>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes</artifactId>
+		<version>3.1.0-incubating-SNAPSHOT</version>
+	</parent>
+
+
+	<dependencies>
+		<dependency>
+			<groupId>net.sf.mastif</groupId>
+			<artifactId>mastif-zoner</artifactId>
+			<version>1.4</version>
+		</dependency>
+    <!--
+		<dependency>
+			<groupId>org.mitre.medfacts</groupId>
+			<artifactId>medfacts-zoner</artifactId>
+			<version>1.1</version>
+			<scope>system</scope>
+			<systemPath>${project.basedir}/lib/med-facts-zoner-1.1.jar</systemPath>
+		</dependency>
+    -->
+		<dependency>
+      <groupId>org.apache.uima</groupId>
+      <artifactId>uimaj-core</artifactId>
+		</dependency>
+
+    <!--
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-type-system</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-utils</artifactId>
+		</dependency>
+		<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</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-util</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.cleartk</groupId>
+			<artifactId>cleartk-test-util</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.cleartk</groupId>
+			<artifactId>cleartk-eval</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.cleartk</groupId>
+			<artifactId>cleartk-examples</artifactId>
+			<exclusions>
+				<exclusion>
+				<!- - Excluding mallet/trove4j dependencies due to 
+				licence in compatible until we could remove the
+				cleartk-examples dependency. - ->
+					<groupId>org.cleartk</groupId>
+	          		<artifactId>cleartk-ml-mallet</artifactId>
+	          	</exclusion>
+			</exclusions>
+		</dependency>			
+		<dependency>
+			<groupId>args4j</groupId>
+			<artifactId>args4j</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>commons-io</groupId>
+			<artifactId>commons-io</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>commons-lang</groupId>
+			<artifactId>commons-lang</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>commons-logging</groupId>
+			<artifactId>commons-logging</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.google.guava</groupId>
+			<artifactId>guava</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>commons-cli</groupId>
+			<artifactId>commons-cli</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.carrotsearch</groupId>
+			<artifactId>hppc</artifactId>
+		</dependency>
+
+
+		<dependency>
+			<groupId>jdom</groupId>
+			<artifactId>jdom</artifactId>
+		</dependency>
+
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+		</dependency>
+
+				<dependency>
+			<groupId>log4j</groupId>
+			<artifactId>log4j</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.opennlp</groupId>
+			<artifactId>opennlp-maxent</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.opennlp</groupId>
+			<artifactId>opennlp-tools</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.lucene</groupId>
+			<artifactId>lucene-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>tw.edu.ntu.csie</groupId>
+			<artifactId>libsvm</artifactId>
+		</dependency>
+
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-core</artifactId>
+		</dependency>
+
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.uimafit</groupId>
+			<artifactId>uimafit</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-lang</groupId>
+			<artifactId>scala-library</artifactId>
+			<version>2.9.0</version>
+		</dependency>
+		<dependency>
+			<groupId>org.scala-tools.sbinary</groupId>
+			<artifactId>sbinary_2.9.0</artifactId>
+			<version>0.4.0</version>
+		</dependency>
+
+		<!- - Dependencies that still need to be uploaded to Maven Central; when 
+			done, the dependency versions should be moved into the parent pom - ->
+		<dependency>
+			<groupId>org.mitre.medfacts</groupId>
+			<artifactId>medfacts-i2b2</artifactId>
+			<version>1.2</version>
+			<scope>system</scope>
+			<systemPath>${project.basedir}/lib/med-facts-i2b2-1.2-SNAPSHOT.jar</systemPath>
+		</dependency>
+		<dependency>
+			<groupId>org.mitre.medfacts</groupId>
+			<artifactId>medfacts-zoner</artifactId>
+			<version>1.1</version>
+			<scope>system</scope>
+			<systemPath>${project.basedir}/lib/med-facts-zoner-1.1.jar</systemPath>
+		</dependency>
+		<dependency>
+			<groupId>org.mitre.jcarafe.core</groupId>
+			<artifactId>jcarafe.core</artifactId>
+			<version>2.9.1</version>
+			<scope>system</scope>
+			<systemPath>${project.basedir}/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar</systemPath>
+		</dependency>
+		<dependency>
+			<groupId>org.mitre.jcarafe.ext</groupId>
+			<artifactId>jcarafe.ext</artifactId>
+			<version>2.9.1</version>
+			<scope>system</scope>
+			<systemPath>${project.basedir}/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar</systemPath>
+		</dependency>
+    -->
+	</dependencies>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.cleartk</groupId>
+				<artifactId>jcasgen-maven-plugin</artifactId>
+				<configuration>
+					<typeSystem>src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml</typeSystem>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>
+</project>

Added: incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/RunZoner.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/RunZoner.java?rev=1425006&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/RunZoner.java (added)
+++ incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/RunZoner.java Fri Dec 21 16:30:48 2012
@@ -0,0 +1,163 @@
+package org.mitre.medfacts.uima;
+
+import java.io.File;
+import java.io.FilenameFilter;
+import java.io.IOException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.logging.Logger;
+
+import org.apache.ctakes.core.util.CtakesFileNamer;
+import org.apache.ctakes.core.ae.DocumentIdPrinterAnalysisEngine;
+import org.apache.ctakes.core.cr.XMIReader;
+import org.apache.uima.UIMAException;
+import org.apache.uima.analysis_engine.AnalysisEngineDescription;
+import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.resource.DataResource;
+import org.apache.uima.resource.ExternalResourceDescription;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.apache.uima.resource.SharedResourceObject;
+import org.apache.uima.resource.metadata.TypeSystemDescription;
+import org.uimafit.component.xwriter.XWriter;
+import org.uimafit.factory.AggregateBuilder;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.factory.CollectionReaderFactory;
+import org.uimafit.factory.ExternalResourceFactory;
+import org.uimafit.factory.TypeSystemDescriptionFactory;
+import org.uimafit.factory.UimaContextFactory;
+import org.uimafit.pipeline.SimplePipeline;
+
+public class RunZoner
+{
+  private static Logger logger = Logger.getLogger(RunZoner.class.getName());
+  
+  File inputDirectory;
+  List<File> inputFiles;
+
+  File outputDirectory;
+  
+  public static void main(String args[]) throws UIMAException, IOException, URISyntaxException
+  {
+    if (args.length != 2)
+    {
+      System.err.format("Syntax: %s input_directory output_directory%n", RunZoner.class.getName());
+    }
+    
+    File inputDirectory = new File(args[0]);
+    File outputDirectory = new File(args[1]);
+    
+    List<File> inputFiles = listContents(inputDirectory);
+    
+    RunZoner runner = new RunZoner();
+    runner.setInputDirectory(inputDirectory);
+    runner.setInputFiles(inputFiles);
+    runner.setOutputDirectory(outputDirectory);
+    
+    runner.execute();
+  }
+  
+  public static List<File> listContents(File inputDirectory)
+  {
+    File fileArray[] = inputDirectory.listFiles(new FilenameFilter()
+    {
+      
+      @Override
+      public boolean accept(File dir, String name)
+      {
+        return name.endsWith(".xmi");
+      }
+    });
+    
+    List<File> fileList = Arrays.asList(fileArray);
+    return fileList;
+  }
+
+  public void execute() throws UIMAException, IOException, URISyntaxException
+  {
+    AggregateBuilder builder = new AggregateBuilder();
+    
+    TypeSystemDescription typeSystemDescription = TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath();
+    
+    CollectionReader reader = 
+        CollectionReaderFactory.createCollectionReader(
+          XMIReader.class,
+          typeSystemDescription,
+          XMIReader.PARAM_FILES,
+          inputFiles);
+    
+      AnalysisEngineDescription documentIdPrinter =
+          AnalysisEngineFactory.createPrimitiveDescription(DocumentIdPrinterAnalysisEngine.class);
+      builder.add(documentIdPrinter);
+    
+      URI generalSectionRegexFileUri =
+        this.getClass().getClassLoader().getResource("org/mitre/medfacts/zoner/section_regex.xml").toURI();
+//      ExternalResourceDescription generalSectionRegexDescription = ExternalResourceFactory.createExternalResourceDescription(
+//          SectionRegexConfigurationResource.class, new File(generalSectionRegexFileUri));
+      AnalysisEngineDescription zonerAnnotator =
+          AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
+              ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
+              generalSectionRegexFileUri
+              );
+      builder.add(zonerAnnotator);
+
+      URI mayoSectionRegexFileUri =
+          this.getClass().getClassLoader().getResource("org/mitre/medfacts/zoner/mayo_sections.xml").toURI();
+//        ExternalResourceDescription mayoSectionRegexDescription = ExternalResourceFactory.createExternalResourceDescription(
+//            SectionRegexConfigurationResource.class, new File(mayoSectionRegexFileUri));
+      AnalysisEngineDescription mayoZonerAnnotator =
+          AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
+              ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
+              mayoSectionRegexFileUri
+              );
+      builder.add(mayoZonerAnnotator);
+
+      AnalysisEngineDescription xWriter = AnalysisEngineFactory.createPrimitiveDescription(
+          XWriter.class,
+          typeSystemDescription,
+          XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
+          outputDirectory.toString(),
+          XWriter.PARAM_FILE_NAMER_CLASS_NAME,
+          CtakesFileNamer.class.getName()
+          );
+      
+      builder.add(xWriter);
+
+    logger.info("BEFORE RUNNING PIPELINE...");
+    SimplePipeline.runPipeline(reader,  builder.createAggregateDescription());
+    logger.info("AFTER RUNNING PIPELINE...COMPLETED");
+  }
+
+  public File getInputDirectory()
+  {
+    return inputDirectory;
+  }
+
+  public void setInputDirectory(File inputDirectory)
+  {
+    this.inputDirectory = inputDirectory;
+  }
+
+  public List<File> getInputFiles()
+  {
+    return inputFiles;
+  }
+
+  public void setInputFiles(List<File> inputFiles)
+  {
+    this.inputFiles = inputFiles;
+  }
+
+  public File getOutputDirectory()
+  {
+    return outputDirectory;
+  }
+
+  public void setOutputDirectory(File outputDirectory)
+  {
+    this.outputDirectory = outputDirectory;
+  }
+  
+}

Added: incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/ZoneAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/ZoneAnnotator.java?rev=1425006&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/ZoneAnnotator.java (added)
+++ incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/ZoneAnnotator.java Fri Dec 21 16:30:48 2012
@@ -0,0 +1,136 @@
+package org.mitre.medfacts.uima;
+
+import java.io.IOException;
+import java.net.URI;
+import java.util.Iterator;
+import java.util.List;
+import java.util.logging.Logger;
+
+import org.apache.ctakes.assertion.zoner.types.Heading;
+import org.apache.ctakes.assertion.zoner.types.Subzone;
+import org.apache.ctakes.assertion.zoner.types.Zone;
+import org.apache.uima.UimaContext;
+//import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.resource.DataResource;
+import org.apache.uima.resource.ResourceAccessException;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.apache.uima.resource.SharedResourceObject;
+
+//import org.mitre.medfacts.zoner.*;
+import org.mitre.medfacts.zoner.ZonerCli;
+import org.mitre.medfacts.zoner.ZonerCli.HeadingRange;
+import org.mitre.medfacts.zoner.ZonerCli.Range;
+//import org.mitre.medfacts.zoner.ZonerCliSimplified;
+//import org.mitre.medfacts.zoner.ZonerCliSimplified.HeadingRange;
+//import org.mitre.medfacts.zoner.ZonerCliSimplified.Range;
+import org.uimafit.component.JCasAnnotator_ImplBase;
+import org.uimafit.descriptor.ConfigurationParameter;
+import org.uimafit.descriptor.ExternalResource;
+import org.uimafit.descriptor.TypeCapability;
+
+@TypeCapability(outputs =
+{
+  "org.apache.ctakes.assertion.zoner.types.Zone",
+  "org.apache.ctakes.assertion.zoner.types.Zone:label",
+  "org.apache.ctakes.assertion.zoner.types.Subzone",
+  "org.apache.ctakes.assertion.zoner.types.Subzone:label",
+  "org.apache.ctakes.assertion.zoner.types.Heading",
+  "org.apache.ctakes.assertion.zoner.types.Heading:label"
+})
+
+public class ZoneAnnotator extends JCasAnnotator_ImplBase {
+	public static final String PARAM_SECTION_REGEX_FILE_URI = "SectionRegex";
+	
+  @ConfigurationParameter(
+      name = PARAM_SECTION_REGEX_FILE_URI,
+      description = "xml configuration file with zone regular expression values",
+      mandatory = true)
+  protected URI sectionRegexFileUri;
+
+  protected final Logger logger = Logger.getLogger(ZoneAnnotator.class.getName());
+	
+	//private ZonerCliSimplified zonerCli;
+	
+	@Override
+	public void initialize (UimaContext aContext) throws ResourceInitializationException {
+		super.initialize(aContext);
+		// Create ZonerCli using the resource URI 
+//		URI uri;
+//		try {
+//			uri = getContext().getResourceURI(PARAM_SECTION_REGEX_FILE_NAME);
+//		} catch (ResourceAccessException e) {
+//			e.printStackTrace();
+//			throw new ResourceInitializationException(e);
+//		}
+		//zonerCli = new ZonerCliSimplified(sectionRegexFileUri);
+
+	}
+	
+	private int countOfIndexOutOfBounds = 0;
+
+	@Override
+	public void process(JCas jcas) throws AnalysisEngineProcessException {
+//	  ZonerCliSimplified zonerCli =
+//	      new ZonerCliSimplified(sectionRegexFileUri);
+    ZonerCli zonerCli =
+      new ZonerCli(sectionRegexFileUri);
+    
+		zonerCli.setEntireContents(jcas.getDocumentText());
+		// initialize converter once contents are set
+		zonerCli.initialize();
+		try {
+			zonerCli.execute();
+		} catch (IOException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+			return;
+			//throw new AnalysisEngineProcessException(e);
+		} catch (StringIndexOutOfBoundsException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+			System.out.format("string index out of bounds exception count: %d%n", ++countOfIndexOutOfBounds);
+			return;
+			//throw new AnalysisEngineProcessException(e);
+		}
+		// Add the zone annotations
+		List<Range> rangeList = zonerCli.getRangeList();
+		for (Iterator<Range> i = rangeList.iterator(); i.hasNext();  ) {
+			Range r = i.next();
+		    Zone zAnnot = new Zone(jcas);	
+		    zAnnot.setBegin(r.getBegin());
+		    zAnnot.setEnd(r.getEnd());
+		    zAnnot.setLabel(r.getLabel());
+		    zAnnot.addToIndexes();
+		    logger.info(String.format("added new zone annotation [%d-%d] \"%s\"", zAnnot.getBegin(), zAnnot.getEnd(), zAnnot.getCoveredText()));
+		}
+		
+		List<Range> subsectionRangeList = zonerCli.getSubsections();
+		for (Iterator<Range> i = subsectionRangeList.iterator(); i.hasNext();  ) {
+			Range r = i.next();
+		    Subzone sAnnot = new Subzone(jcas);	
+		    sAnnot.setBegin(r.getBegin());
+		    sAnnot.setEnd(r.getEnd());
+		    sAnnot.setLabel(r.getLabel());
+		    sAnnot.addToIndexes();
+		    logger.info(String.format("added new subzone annotation [%d-%d] \"%s\"", sAnnot.getBegin(), sAnnot.getEnd(), sAnnot.getCoveredText()));
+		}
+		
+		
+		
+		// Add the heading annotations
+		List<HeadingRange> headings = zonerCli.getHeadings();
+		for (Iterator<HeadingRange> i = headings.iterator(); i.hasNext();  ) {
+			HeadingRange r = i.next();
+		    Heading hAnnot = new Heading(jcas);	
+		    hAnnot.setBegin(r.getHeadingBegin());
+		    hAnnot.setEnd(r.getHeadingEnd());
+		    hAnnot.setLabel(r.getLabel());
+		    hAnnot.addToIndexes();
+		    logger.info(String.format("added new headingrange annotation [%d-%d] \"%s\"", hAnnot.getBegin(), hAnnot.getEnd(), hAnnot.getCoveredText()));
+		}
+
+	}
+
+}

Propchange: incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/ZoneAnnotator.java
------------------------------------------------------------------------------
    svn:executable = *

Added: incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/META-INF/org.uimafit/types.txt
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/META-INF/org.uimafit/types.txt?rev=1425006&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/META-INF/org.uimafit/types.txt (added)
+++ incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/META-INF/org.uimafit/types.txt Fri Dec 21 16:30:48 2012
@@ -0,0 +1 @@
+classpath*:org/apache/ctakes/assertion/zoner/types/TypeSystem.xml

Added: incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml?rev=1425006&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml (added)
+++ incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml Fri Dec 21 16:30:48 2012
@@ -0,0 +1,66 @@
+<?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.assertion.types.TypeSystem</name>
+  <description/>
+  <version>1.0</version>
+  <vendor/>
+  <types>
+    <typeDescription>
+      <name>org.apache.ctakes.assertion.zoner.types.Heading</name>
+      <description>a section heading</description>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+      <features>
+        <featureDescription>
+          <name>label</name>
+          <description/>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+      </features>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.assertion.zoner.types.Zone</name>
+      <description>A document Zone, including its heading</description>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+      <features>
+        <featureDescription>
+          <name>label</name>
+          <description/>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+      </features>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.assertion.zoner.types.Subzone</name>
+      <description/>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+      <features>
+        <featureDescription>
+          <name>label</name>
+          <description/>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+      </features>
+    </typeDescription>
+  </types>
+</typeSystemDescription>
+

Added: incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/mitre/medfacts/uima/section_regex.04162012.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/mitre/medfacts/uima/section_regex.04162012.xml?rev=1425006&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/mitre/medfacts/uima/section_regex.04162012.xml (added)
+++ incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/mitre/medfacts/uima/section_regex.04162012.xml Fri Dec 21 16:30:48 2012
@@ -0,0 +1,641 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<root>
+<fragments> 
+<!-- Modifier Components of Section Headings -->
+  <fragment>
+    <name>admit</name>
+    <expansion>(?:admit(?:ting)?|admission)</expansion>
+  </fragment>
+<fragment>
+  <name>be</name>
+  <expansion>(\s+(?:am|is|are|was|were))</expansion>
+</fragment>
+  <fragment>
+    <name>left-time-mods</name>  
+    <expansion>((?:(?:pre-)?<fragment-ref name="admit"/>|current|discharge|follow[\s+\-]?up|home|interim|initial|postpartum|(?:pre|post)op(?:erative)?|transfer)\s+)</expansion>
+  </fragment>
+  <fragment>
+    <name>left-descr-mods</name>  
+    <expansion>((?:brief(?:\s+resume\s+of)?|overall|other|additional|pertinent|relevant|(?:list\s+of\s+)?other|plan\s+for|standardized|summary\s+of|doctor(?:\s+\&apos;)?s)\s+)</expansion>
+  </fragment>
+<fragment>
+  <name>include</name>
+  <expansion>(\s+(?:include[ds]?))</expansion>
+</fragment>
+  <fragment>
+    <name>right-time-mods</name>
+    <expansion>(\s+(?:(?:(?:UP)?ON|AS|AT|\@|OF|FOR|(?:PRIOR\s+TO)|(?:DURING))\s+(?:(?:(?:THE|THAT|THIS)\s+)?(?:TIME|DAY)\s+OF\s+)?(?:ADMISSION|ADMIT|DEATH|DISCHARGE|TRANSFER|COMPLICATIONS?|HOME|HOSPITALIZATION|OUTPATIENT)))</expansion>
+  </fragment>
+  <fragment>
+    <name>right-descr-mods</name>
+    <expansion>(\s+(?:(?:by\s+(?:problems?|(?:organ\s+)?systems?|issues?|report))|(?:\s+of\s+note)))</expansion>
+  </fragment>
+  <fragment>
+    <name>right-location-mods</name>
+    <expansion>(\s+in\s+the\s+emergency\s+department)</expansion>
+  </fragment>
+<!-- Core Components of Section Headings -->
+<!--HISTORY/SUBJECTIVE-->
+  <fragment>
+    <name>allergies1</name>
+    <expansion>(?:allergies|allergy|adverse\s+drug\s+reactions?)</expansion>
+  </fragment>
+  <fragment>
+    <name>allergies2</name>
+    <expansion>(allergy(\s*\/\s*reaction)?\s+profile)</expansion>
+  </fragment>
+  <fragment>
+    <name>famhistory</name>
+    <expansion>(?:family\s+(?:(?:medical|social)\s+)?history|fhx?|fam\s+hx)</expansion>
+  </fragment>
+  <fragment>
+    <name>sochistory</name>
+    <expansion>(social\s+history|social\s+hx|\bshx?|soc\s*hx|habits)</expansion>
+  </fragment>
+<!--MEDICATIONS-->
+  <fragment>
+    <name>medication1</name>       
+    <expansion>(medications?|medication\s*\(\s*s\s*\)|regimen|treatment\s+cycle)</expansion>
+  </fragment>
+  <fragment>
+    <name>medication2</name>
+    <expansion>(meds?)</expansion>
+  </fragment>
+<!--EXAM/LAB/OBJECTIVE-->
+  <fragment>
+    <name>physicalexam1</name>
+    <expansion>((physical|surgical)(\s+exam(ination)?|\s+findings)?|\bpe|\*pe|on\s+exam(ination)?|examination\s+data)</expansion>
+  </fragment>
+  <fragment>
+    <name>physicalexam2</name>
+    <expansion>((daily|patient)\s+status)</expansion>
+  </fragment>
+<!--ASSESSMENT/DISPOSITION/PLAN/INSTRUCTIONS-->
+<!--IN-PATIENT COURSE-->
+<!--DIAGNOSIS-->
+<!--PROCEDURE/TREATMENT-->
+<!--MAYO CLINIC STYLE DATE -->
+  <fragment>
+    <name>time</name>
+    <expansion>(\d?\d\:\d\d[aApP][mM])</expansion>
+  </fragment>
+  <fragment>
+    <name>mayodate</name>
+    <expansion>(([0123])?\d(Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec)(\d\d)?\d\d\s+<fragment-ref name="time"/>)</expansion>
+  </fragment>
+  <fragment>
+    <name>mayodate2</name>
+    <expansion>([01]?\d/\d?\d/(\d\d)?\d\d\s+<fragment-ref name="time"/>)</expansion>
+  </fragment>
+</fragments>
+
+<!-- Section Heading Patterns -->
+<sections>
+  <!-- ADDENDUM --> 
+  <section>
+    <regex>((addendum)\s*\:)</regex>
+    <label>addendum</label>
+  </section>
+  <!-- ADMISSION DATE --> 
+  <section>
+    <regex>(?:(?:(?:admission\s+date)|(date\s+of\s+admission))\s*\:)</regex>
+    <label>admission date</label>
+  </section>
+  <!-- AGE --> 
+  <section>
+    <regex>age\s*\:</regex>
+    <label>age</label>
+  </section>
+  <!-- ALLERGY --> 
+  <section>
+    <regex>(?:(?:<fragment-ref name="allergies1"/>|<fragment-ref name="allergies2"/>)\s*\:)</regex>
+    <label>allergy</label>
+  </section>
+  <!-- APPOINTMENTS --> 
+  <section>
+    <regex>(((<fragment-ref name="left-time-mods"/>)|(<fragment-ref name="left-descr-mods"/>))?(appointments?(?:\(?:\s+s\s+\))?)\s*(?:\(\s+s\s+\))?\s*\:)</regex>
+    <label>appointments</label>
+  </section>
+  <!-- ASSESSMENT --> 
+  <section>
+    <regex>((<fragment-ref name="left-time-mods"/>|<fragment-ref name="left-descr-mods"/>)?(assessment)(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+    <label>assessment</label>
+  </section>
+   <!-- ASSESSMENT/PLAN --> 
+  <section>
+    <regex>(((<fragment-ref name="left-time-mods"/>)|<fragment-ref name="right-descr-mods"/>)?((?:assessment\s*(?:and|\&amp;|\/)\s*plan)|(?:a\s*(?:\&amp;|\/)\s*p))(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+    <label>assessment/plan</label>
+  </section>
+  <!-- ATTENDING MD --> 
+  <section>
+    <regex>(?:attend(?:ing)?(?:\s+physician)?\s*\:)</regex>
+    <label>attending md</label>
+  </section>
+  <section>
+    <regex ignore-case="false">([A-Z]{2,2}\d{3,3}\/\d{4,4}\s+[A-Z]+\s+([A-Z]\.\s+)?[A-Z]+\s+\,(?:\s+(?:jr|iii)\s*\,\s*)?\s+M\.D\.)\s*\:</regex>
+    <label>attending md</label>
+  </section>
+  <!-- CHIEF COMPLAINT --> 
+  <section>
+    <regex find-all="false">(?:(?:chief\s+complaint)|(?:patient\s+states\s+complaint)\s*\:)</regex>
+    <label>chief complaint</label>
+  </section>
+  <!-- CLINICAL FINDINGS --> 
+  <section>
+    <regex>((clinical\s+findings?)\s*\:)</regex>
+    <label>clinical findings</label>
+  </section>
+  <!-- CODE STATUS --> 
+  <section>
+    <regex find-all="false">(?:((code(?:\s+status)?)\s*\:))</regex>
+    <label>code status</label>
+  </section>
+  <!-- COMMENTS --> 
+  <section>
+    <regex>(((?:additional\s+)comments)\s*\:)</regex>
+    <label>comments</label>
+  </section>
+  <!-- COMPLICATIONS --> 
+  <section>
+    <regex find-all="false">(?:((complications?)\s*\:))</regex>
+    <label>complications</label>
+  </section>
+  <!--CONDITION  --> 
+  <section>
+    <regex>((<fragment-ref name="left-time-mods"/>)?(condition)(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+    <label>condition</label>
+  </section>
+  <!-- CONSULTANTS --> 
+  <section>
+    <regex>((consultants?)\s*\:)</regex>
+    <label>consultants</label>
+  </section>
+  <!-- CONSULTATION SUMMARY --> 
+  <section>
+    <regex>((consults)\s*\:)</regex>
+    <label>consultation summary</label>
+  </section>
+  <!--DATE OF BIRTH  --> 
+  <section>
+    <regex>date\s+of\s+birth\s*\:</regex>
+    <label>date of birth</label>
+  </section>
+  <!--DATE OF EXPIRATION  --> 
+  <section>
+    <regex>date\s+of\s+expiration\s*\:</regex>
+    <label>date of expiration</label>
+  </section>
+  <!-- DIAGNOSES --> 
+  <section>
+    <regex>(((?:principal\s+discharge\s+diagnosis\s*;\s*responsible\s+after\s+study\s+for\s+causing\s+admission\s*\)\s?))\s?)</regex>
+    <label>diagnoses</label>
+  </section>
+  <section>
+    <regex>((?:other\s+diagnosis\s*;\s*conditions\s*\,\s*infections\s*,\s*complications\s*,\s*affecting\s+treatment\s*\/?\s*stay)\s?)</regex>
+    <label>diagnoses</label>
+  </section>
+  <section>
+    <regex>(((?:cause\s+of\s+death\s+and\s+)?((?:final|principal|principle|primary|associated|secondary|additional|other)\s+)?(((?:pre-)?admission|admit(?:ting)?|discharge|(?:pre|post)?operative)\s+)?(?:problems\s+and\s+)?diagnos[ei]s(?:\s*\(\s*es\s*\))?)(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+    <label>diagnoses</label>
+  </section>
+   <!-- DICTATION\/AUTHOR DETAILS --> 
+  <section>
+    <regex>((?:(?:(?:entered|dictated)\s+by\b)|dictator)\s*\:)</regex>
+    <label>dictation/author details</label>
+  </section>
+  <section>
+    <regex ignore-case="false">((?:(?:[A-Z]+\.?)\s+)*[A-Z]+\s*\,\s+M\.D\.\s+DICTATING\s+FOR\s*\:)</regex>
+    <label>dictation/author details</label>
+  </section>
+  <section>
+    <regex ignore-case="false">(This\s+report\s+was\s+created\s+by\s+[A-Z])</regex>
+    <label>dictation/author details</label>
+  </section>
+  <!-- DIET --> 
+  <section>
+    <regex>((<fragment-ref name="left-time-mods"/>)?(diet)\s*\:)</regex>
+    <label>diet</label>
+  </section>
+  <!-- DISCHARGE ACTIVITY --> 
+  <section>
+    <regex>(((?:discharge\s+)?activity)\s*\:)</regex>
+    <label>discharge activity</label>
+  </section>
+  <section>
+    <regex>(^((?:discharge\s+)?activity)\s*)(\n)</regex>
+    <label>discharge activity</label>
+  </section>
+  <!-- DISCHARGE DATE --> 
+  <section>
+    <regex>((discharge\s+date)|(date\s+of\s+discharge))\s*\:</regex>
+    <label>discharge date</label>
+  </section>
+  <!-- DISCHARGE DETAILS --> 
+  <section>
+    <regex>((discharge\s+patient\s+on)\s*\:)</regex>
+    <label>discharge details</label>
+  </section>
+   <!-- DISCHARGE ORDERS --> 
+  <section>
+    <regex>(((?:doctor\'?s\s+)?discharge\s+orders)\s*\:)</regex>
+    <label>discharge orders</label>
+  </section>
+  <!-- DISCHARGE NOTIFICATION SUMMARY --> 
+  <section>
+    <regex>(ed\s+discharge\s+notification\s*\/\s*summary)(\s+)</regex>
+    <label>discharge notification summary</label>
+  </section>
+  <!-- DISPOSITION --> 
+  <section>
+    <regex>((<fragment-ref name="left-time-mods"/>)?(disposition)(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+    <label>disposition</label>
+  </section>
+  <!-- EMERGENCY DEPARTMENT COURSE --> 
+  <section>
+    <regex>((<fragment-ref name="left-descr-mods"/>)?((?:ed\s+course)|(?:emergency\s+department\s+course)|(?:in\s+(?:the\s+)?ed|\bed))<fragment-ref name="right-descr-mods"/>?(\s*\:|\*+))</regex>
+    <label>emergency department course</label>
+  </section>
+  <!-- EVALUATION DATE --> 
+  <section>
+    <regex>evaluation\s+date\s*\:</regex>
+    <label>evaluation date</label>
+  </section>
+   <!-- EVENTS --> 
+  <section>
+    <regex>((events)\s*\:)</regex>
+    <label>events</label>
+  </section>
+  <!-- FAMILY HISTORY --> 
+  <section>
+    <regex find-all="false">(?:(?:<fragment-ref name="famhistory"/>)\s*\:)</regex>
+    <label>family history</label>
+  </section>
+  <section>
+    <regex ignore-case="false" find-all="false">(?:(?:FAMILY\s+HISTORY\s+[a-z]+))</regex>
+    <label>family history</label>
+  </section>
+  <!-- FOLLOW-UP --> 
+  <section>
+    <regex>((discharged?\s+wound\s+care)\s*\:)</regex>
+    <label>discharge wound care</label>
+  </section>
+  <section>
+    <regex>(((?:discharged?\s+follow[\s\-]?up(?:\s+care)?)|((?:standardized\s+)?discharge\s+orders\s+\(\s+medications\s+instructions\s+to\s+patient\s+\,\s+follow-up\s+care\s+\))|(disposition\s*\,\s+follow[\s+\-]up\s+and\s+instructions\s+to\s+patient)|(?:follow[\s\-]?up))\s*\:)</regex>
+    <label>follow-up</label>
+  </section>
+  <section>
+    <regex>((((?:discharged?\s+follow[\s\-]?up(?:\s+care)?))|((?:standardized\s+)?discharge\s+orders\s+\(\s+medications\s+instructions\s+to\s+patient\s+\,\s+follow-up\s+care\s+\))|(disposition\s*\,\s+follow[\s+\-]up\s+and\s+instructions\s+to\s+patient)|(?:follow[\s\-]?up))\s*)(\n)</regex>
+    <label>follow-up</label>
+  </section>
+  <!-- GENDER --> 
+  <section>
+    <regex>sex\s*\:</regex>
+    <label>gender</label>
+  </section>
+  <!-- HEALTH STATUS --> 
+  <section>
+    <regex>^(health\s+status)\s*(\n)</regex>
+    <label>health status</label>
+  </section>
+  <!-- HISTORY OF PRESENT ILLNESS/REASON FOR HOSPITALIZATION --> 
+  <section>
+    <regex>((<fragment-ref name="left-descr-mods"/>)?(?:history\s+(?:of\s+(?:the\s+)?)?(?:present|physical)\s+illness|hpi)\s+and\s+(?:(?:history\s+and\s+)?reasons?\s+(?:for\s+)?(?:hospitalization|admission|admit))\s*\:)</regex>
+    <label>history of present illness/reason for hospitalization</label>
+  </section>
+  <section>
+    <regex find-all="false">((?:(?:history\s+and\s+)?reasons?\s+(?:for\s+)?(?:hospitalization|admission|admit))\s*\:)</regex>
+    <label>reason for hospitalization</label>
+  </section>
+  <section>
+    <regex>((<fragment-ref name="left-descr-mods"/>)?(((history\s+(of\s+(the\s+)?)?)?(present|physical)\s+illness)|hpi)\s*\:)</regex>
+    <label>history of present illness</label>
+  </section>
+  <section>
+    <regex>(((?:history\s+(?:of\s+(?:the\s+)?)?(?:present|physical)\s+illness)|hpi)\s*)\n</regex>
+    <label>history of present illness</label>
+  </section>
+  <section>
+    <regex>(^(<fragment-ref name="left-descr-mods"/>)?((?:clinical\s+)?history)\s*\:)</regex>
+    <label>history of present illness</label>
+  </section>
+  <!-- HOSPITAL COURSE --> 
+  <section>
+    <regex>((<fragment-ref name="left-descr-mods"/>)?(?:hosp(?:ital)?\s+course(?:\s+and\s+treatment)?)|(?:summary\s+of\s+hospitalization)<fragment-ref name="right-descr-mods"/>?(\s*\:|\*+|\-+))</regex>
+    <label>hospital course</label>
+  </section>
+  <section>
+    <regex>((<fragment-ref name="left-descr-mods"/>)?(?:hosp(?:ital)?\s+course(?:\s+and\s+treatment)?)|(?:summary\s+of\s+hospitalization)<fragment-ref name="right-descr-mods"/>?)(\s*\n)</regex>
+    <label>hospital course</label>
+  </section>
+  <section>
+    <regex>(\*+(hosp(?:ital)?\s+course(?:\s+and\s+treatment)?)|(?:summary\s+of\s+hospitalization))</regex>
+    <label>hospital course</label>
+  </section>
+  <section>
+    <regex>((hosp(?:ital)?\s+course(\s+and\s+treatment)?)|(summary\s+of\s+hospitalization)<fragment-ref name="right-descr-mods"/>\s+([a-z]+|\())</regex>
+    <label>hospital course</label>
+  </section>
+  <!-- IMPRESSION --> 
+  <section>
+    <regex find-all="false">((impressions?|imp)(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+    <label>impression</label>
+  </section>
+ <!-- IMPRESSION\/PLAN --> 
+  <section>
+    <regex>((?:impression\s+and\s+plan)\s*\:)</regex>
+    <label>impression/plan</label>
+  </section>
+  <!-- IMPRESSION\/PLAN --> 
+  <section>
+    <regex>((?:impression\s+and\s+plan)\s*)(\n)</regex>
+    <label>impression/plan</label>
+   </section>
+  <!-- INSTRUCTIONS --> 
+  <section>
+    <regex>(((<fragment-ref name="left-time-mods"/>)|(<fragment-ref name="left-descr-mods"/>))+(instructions?)(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+    <label>instructions</label>
+  </section>
+   <section>
+    <regex>(^(instructions?)(<fragment-ref name="right-time-mods"/>)?\s*)(\n)</regex>
+    <label>instructions</label>
+  </section>
+  <!--LABORATORY/STUDIES  --> 
+  <section>
+    <regex>((?:(<fragment-ref name="left-time-mods"/>)|(<fragment-ref name="left-descr-mods"/>))?((?:summary\s+of\s+)?(?:(?:diagnostic\s+)?(?:laboratory|labs?|laboratories|diagnostic|radiologic)(?:(?:\s+and\s+)|(?:\/))?\s*(?:radiologic\s+)?(?:studies|data|results|exams?(?:inations?)?|evaluation|values|findings|tests?|x\-rays?)?)|(?:tests\/procedures|(?:studies\/(?:procedures|tests))|(?:proc(?:edures)?\/tests)|tests))(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+    <label>laboratory</label>
+  </section>
+  <section>
+    <regex>(((?:new|discrete|(?:today\s+\'s))\s+results(?:\s+only)?)\s*\:)</regex>
+    <label>laboratory</label>
+  </section>
+  <section>
+    <regex>(((?:new|discrete|(?:today\s+\'s))\s+results(?:\s+only)?)\s*)\n</regex>
+    <label>laboratory</label>
+  </section>
+  <section>
+    <regex>((<fragment-ref name="left-time-mods"/>)\s*data(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+    <label>laboratory</label>
+  </section>
+  <section>
+    <regex>((?:\-+|\*+|\_+)\s*)(data(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+    <label>laboratory</label>
+  </section>
+  <!-- MEDICATION --> 
+  <section>
+    <regex>(<fragment-ref name="left-time-mods"/>)?(<fragment-ref name="medication1"/>)(<fragment-ref name="right-time-mods"/>)?(<fragment-ref name="be"/>|<fragment-ref name="include"/>)?\s*\:</regex>
+    <label>medication</label>
+  </section>
+  <section>
+    <regex>^(<fragment-ref name="left-time-mods"/>)?(<fragment-ref name="medication1"/>)(<fragment-ref name="right-time-mods"/>)?(<fragment-ref name="be"/>|<fragment-ref name="include"/>)?\s*\n</regex>
+    <label>medication</label>
+  </section>
+  <section>
+     <regex>(<fragment-ref name="left-time-mods"/>)(<fragment-ref name="medication2"/>)(<fragment-ref name="right-time-mods"/>)?(<fragment-ref name="be"/>|<fragment-ref name="include"/>?\s*\:)</regex>
+    <label>medication</label>
+  </section>
+  <section>
+     <regex>^(<fragment-ref name="medication2"/>)(<fragment-ref name="right-time-mods"/>)?(<fragment-ref name="be"/>|<fragment-ref name="include"/>?\s*\:)</regex>
+    <label>medication</label>
+  </section>
+  <section>
+    <regex>((<fragment-ref name="left-time-mods"/>)?(<fragment-ref name="medication1"/>)\s+on\s+transfer\s+from(\s+[A-Z]+)+(<fragment-ref name="be"/>|<fragment-ref name="include"/>)?\s*\:)</regex>
+    <label>medication</label>
+  </section>
+  <section>
+    <regex ignore-case="false" >(MEDICATIONS(<fragment-ref name="right-time-mods"/>)?)(\s+[a-z]+)</regex>
+    <label>medication</label>
+  </section>
+  <!--OB-GYN HISTORY  --> 
+  <section>
+    <regex>(((?:(?:past\s+)?ob\-gyn\s+history))\s*\:)</regex>
+    <label>ob-gyn history</label>
+  </section>
+  <section>
+    <regex>(((?:past\s+obstetric\s+history))\s*\:)</regex>
+    <label>obstetric history</label>
+  </section>
+  <section>
+    <regex>^(((?:past\s+gyn(?:ocologic(?:al)?)?\s+history))\s*\:)</regex>
+    <label>gynocologic history</label>
+  </section>
+  <!-- OBJECTIVE --> 
+  <section>
+    <regex find-all="false">(?:objective\s*\:?\n)</regex>
+    <label>objective</label>
+  </section>
+  <section>
+    <regex find-all="false">(?:^o\s*\:\n)</regex>
+    <label>objective</label>
+  </section>
+  <!--OPERATIONS/PROCEDURES  --> 
+  <section>
+    <regex>(((?:((?:principal|principle|primary|special)\s+)?(?:operations?\s+(?:and|or)\s+)?procedures?(\s+(?:and|or)\s+operations?)?(?:\s+performed)?)|(operations\s*\/\s*procedures)|(?:operations?))\s*\:)</regex>
+    <label>operations/procedures</label>
+  </section>
+  <section>
+    <regex>((((?:associated|secondary|additional|other)\s+)(?:operations?\s+(?:and|or)\s+)?procedures?(\s+(?:and|or)\s+operations?)?)\s*\:)</regex>
+    <label>operations/procedures</label>
+  </section>
+  <section>
+    <regex>((procedure\s+note)\s*\:)</regex>
+    <label>procedure description</label>
+  </section>
+    <section>
+    <regex>((procedure\s+in\s+detail)\s*\:)</regex>
+    <label>procedure description</label>
+  </section>
+  <section>
+    <regex>((postpartum\s+diagnostic\s+procedures)\s*\:)</regex>
+    <label>postpartum diagnostic procedures</label>
+  </section>
+  <section>
+    <regex>((postpartum\s+therapeutic\s+procedures)\s*\:)</regex>
+    <label>postpartum therapeutic procedures</label>
+  </section>
+  <section>
+    <regex>((other\s+postpartum\s+therapies)\s*\:)</regex>
+    <label>other poastpartum treatment</label>
+  </section>
+   <section>
+    <regex>^procedure:\s*$</regex>
+    <label>operations/procedures</label>
+  </section>
+  <!-- PAST CARDIAC HISTORY --> 
+  <section>
+    <regex>((past\s+cardiac\s+history)\s*\:)</regex>
+    <label>past cardiac history</label>
+  </section>
+  <!-- PAST MEDICAL HISTORY --> 
+  <section>
+    <regex>(past\s+(medical\s+)?history|medical\s+history|pmhx?|pmedhx)\s*\:</regex>
+    <label>past medical history</label>
+  </section>
+  <section>
+    <regex>((past\s+(?:medical\s+)?history|medical\s+history|pmhx?|pmedhx)\/(<fragment-ref name="sochistory"/>)\s*\:)</regex>
+    <label>past medical history</label>
+  </section>
+  <!-- PAST SURGICAL HISTORY --> 
+  <section>
+    <regex>(past\s+surgical\s+history)\s*\:</regex>
+    <label>past surgical history</label>
+  </section>
+  <!-- PATIENT INFO --> 
+  <section>
+    <regex ignore-case="false">(\*+\s+(FINAL\s+)?DISCHARGE\s+ORDERS\s+\*+)</regex>
+    <label>patient info</label>
+  </section>
+  <!-- PHYSICAL EXAMINATION --> 
+  <section>
+    <regex>((<fragment-ref name="left-descr-mods"/>)?(<fragment-ref name="left-time-mods"/>)?(<fragment-ref name="physicalexam1"/>|<fragment-ref name="physicalexam2"/>)(<fragment-ref name="right-time-mods"/>)?<fragment-ref name="right-location-mods"/>?(?:\s*\:|\-[^a-z]))</regex>
+    <label>physical examination</label>
+  </section>
+  <section>
+    <regex>((<fragment-ref name="left-descr-mods"/>)?(<fragment-ref name="left-time-mods"/>)?(<fragment-ref name="physicalexam1"/>|<fragment-ref name="physicalexam2"/>)(<fragment-ref name="right-time-mods"/>)?(<fragment-ref name="right-location-mods"/>)?)((\s+vss?)(?:\s*\:|\-[^a-z]))</regex>
+    <label>physical examination</label>
+ </section>
+  <section>
+    <regex>((?:\-+|\*+|\_+|(<fragment-ref name="left-descr-mods"/>))\s*(?:exam(?:ination)?(?:\s+data)?(<fragment-ref name="right-time-mods"/>)\s*\:))</regex>
+    <label>physical examination</label>
+  </section>
+  <section>
+    <regex>^((<fragment-ref name="left-time-mods"/>)(?:exam(?:ination)?)(?:\s*\:))</regex>
+    <label>physical examination</label>
+  </section>
+  <section>
+    <regex>^((<fragment-ref name="left-descr-mods"/>)?(<fragment-ref name="left-time-mods"/>)?(<fragment-ref name="physicalexam1"/>|<fragment-ref name="physicalexam2"/>))(\n)</regex>
+    <label>physical examination</label>
+  </section>
+  <!-- PLAN  --> 
+  <section>
+    <regex ignore-case="false">(?:^((<fragment-ref name="left-time-mods"/>)?(\bplans?)(\s*\:[^\d]|\s*\*)))</regex>
+    <label>plan</label>
+  </section>
+  <section>
+    <regex ignore-case="false">(?:^((<fragment-ref name="left-time-mods"/>)?(\bplans?))(\s*\n))</regex>
+    <label>plan</label>
+  </section>
+  <!-- PLAN: DISPOSITION/PLAN  --> 
+  <section>
+    <regex>(((?:disposition\s*(?:and|\&amp;|\/)\s*plan)|(?:disposition\s*(?:\&amp;|\/)plan))(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+    <label>plan</label>
+  </section>
+  <!-- PLAN: TO DO\/PLAN --> 
+  <section>
+    <regex>(((?:to\s+do\s*\/\s*plans?))\s*\:)</regex>
+    <label>plan</label>
+  </section>
+  <!-- PRELIMINARY REPORT CONTENT --> 
+  <section>
+    <regex>(($pch)\s*\:)(\s+)</regex>
+    <label>preliminary report content</label>
+  </section>
+  <!-- PREOPERATIVE STATUS --> 
+  <section>
+    <regex>((preoperative\s+(?:cardiac\s+)?status)\s*\:)</regex>
+    <label>preoperative stastus</label>
+  </section>
+  <!-- PREVIOUS CARDIOVASCULAR INTERVENTIONS --> 
+  <section>
+    <regex>((previous\s+cardiovascular\s+interventions?)\s*\:)</regex>
+    <label>previous cardiovascular interventions</label>
+  </section>
+  <!-- PRIMARY CARE PHYSICIAN --> 
+  <section>
+    <regex find-all="false">(?:pcp\s+name\s*\:)</regex>
+    <label>primary care physician</label>
+  </section>
+  <!-- PROBLEMS --> 
+  <section>
+    <regex>(((?:(?:patient\s+)?problem\s+list)|(?:significant\s+problems)|(?:(?:(?:his|her)\s+)?problems\s+and\s+management\s+are\s+as\s+follows) )<fragment-ref name="right-descr-mods"/>?\s*[\:;\*+])</regex>
+    <label>problems</label>
+  </section>
+  <!-- RADIOLOGY --> 
+  <section>
+    <regex find-all="false">(?:(?:radiology(?:\s+(?:studies|data|results))?)\s*\:)</regex>
+    <label>radiology</label>
+  </section>
+  <!-- REASON FOR CONSULTATION  --> 
+  <section>
+    <regex find-all="false">(?:reason\s+(?:for\s+)?consultation\s*\:)</regex>
+    <label>reason for consultation</label>
+  </section>
+  <!-- REPORT STATUS --> 
+  <section>
+    <regex>((report\s+status)\s*\:)</regex>
+    <label>report status</label>
+  </section>
+  <!--REVIEW OF SYSTEMS  --> 
+  <section>
+    <regex find-all="false">(?:(review\s+(?:of\s+)?systems|ros)\s*\:)</regex>
+    <label>review of systems</label>
+  </section>
+  <section>
+    <regex ignore-case="false" find-all="false">(?:(REVIEW\s+OF\s+SYSTEMS)(\s+[a-z]+))</regex>
+    <label>review of systems</label>
+  </section>
+  <!-- SERVICE SPRECIALTY --> 
+  <section>
+    <regex find-all="false">(?:service\s*\:)</regex>
+    <label>service specialty</label>
+  </section>
+  <!-- SOCIAL HISTORY --> 
+  <section>
+    <regex>(?:^(<fragment-ref name="sochistory"/>)\s*\:)</regex>
+    <label>social history</label>
+  </section>
+  <section>
+    <regex ignore-case="false" find-all="false">(?:((SOCIAL\s+HISTORY|HABITS))(\s+[a-z]+))</regex>
+    <label>social history</label>
+  </section>
+  <!-- SUBJECTIVE --> 
+  <section>
+    <regex find-all="false">(?:subjective\s*\:?\n)</regex>
+    <label>subjective</label>
+  </section>
+  <section>
+    <regex find-all="false">(?:^s\s*\:\n)</regex>
+    <label>subjective</label>
+  </section>
+  <!-- TRANSCRIPTION DETAILS --> 
+  <section>
+    <regex>(((?:escription\s+document)|batch)\s*\:)</regex>
+    <label>transcription details</label>
+  </section>
+  <!-- TREATMENT --> 
+  <section>
+    <regex>(((?:treatment\s+rendered))\s*\:?)</regex>
+    <label>treatment</label>
+  </section>
+  <section>
+    <regex>((((?:other\s+treatments?\s*\/\s*procedures\s+\(\s+not\s+in\s+o\.r\.\s+\)))|(other\s+treatments?\s+and\s+procedures))\s*\:?)</regex>
+    <label>other treatments/procedures</label>
+  </section>
+  <!-- UNIT NUMBER --> 
+  <section>
+    <regex find-all="false">(?:unit\s+number\s*\:)</regex>
+    <label>unit number</label>
+  </section>
+    <!-- WORK RETURN --> 
+  <section>
+    <regex>((return\s+to\s+work)\s*\:)</regex>
+    <label>work return</label>
+  </section>
+  <!--  SECTIONS for Mayo style radiology reports -->
+  <section>
+    <regex>(?:<fragment-ref name="mayodate"/>\s+Exam\:)</regex>
+    <label>radiology exam type</label>
+  </section>
+  <section>
+    <regex>(?:ORIGINAL REPORT)</regex>
+    <label>radiology exam report</label>
+  </section>
+  <section>
+    <regex>(?:<fragment-ref name="mayodate2"/>\s+\*+\s+Final\s+\*+)</regex>
+  </section>
+  <section>
+    <regex>(?:Indications\:)</regex> 
+    <label>reason for examination</label>
+  </section>
+</sections>
+</root>
+

Propchange: incubator/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/mitre/medfacts/uima/section_regex.04162012.xml
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