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From vjapa...@apache.org
Subject svn commit: r1560995 [2/2] - in /ctakes/branches/ytex/ctakes-ytex-web: ./ .settings/ src/ src/main/ src/main/java/ src/main/java/org/ src/main/java/org/apache/ src/main/java/org/apache/ctakes/ src/main/java/org/apache/ctakes/ytex/ src/main/java/org/apa...
Date Fri, 24 Jan 2014 13:33:11 GMT
Added: ctakes/branches/ytex/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/ConceptSimilarityRestService.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/ConceptSimilarityRestService.java?rev=1560995&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/ConceptSimilarityRestService.java (added)
+++ ctakes/branches/ytex/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/ConceptSimilarityRestService.java Fri Jan 24 13:33:09 2014
@@ -0,0 +1,33 @@
+package org.apache.ctakes.ytex.ws;
+
+import java.util.List;
+
+import javax.ws.rs.GET;
+import javax.ws.rs.Path;
+import javax.ws.rs.Produces;
+import javax.ws.rs.QueryParam;
+
+import org.apache.ctakes.ytex.kernel.metric.ConceptPairSimilarity;
+
+@Path("/rest/")
+@Produces("application/xml")
+public interface ConceptSimilarityRestService {
+	
+	@GET
+	@Path("/getDefaultConceptGraph")
+	public SimServiceInfo getDefaultConceptGraph();
+	
+	@GET
+	@Path("/getConceptGraphs")
+	public List<SimServiceInfo> getConceptGraphs();
+
+
+	@GET
+	@Path("/similarity")
+	public ConceptPairSimilarity similarity(
+			@QueryParam("conceptGraph") String conceptGraph,
+			@QueryParam("concept1") String concept1,
+			@QueryParam("concept2") String concept2,
+			@QueryParam("metrics") String metrics,
+			@QueryParam("lcs") String lcs);
+}

Added: ctakes/branches/ytex/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/ConceptSimilarityWebService.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/ConceptSimilarityWebService.java?rev=1560995&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/ConceptSimilarityWebService.java (added)
+++ ctakes/branches/ytex/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/ConceptSimilarityWebService.java Fri Jan 24 13:33:09 2014
@@ -0,0 +1,33 @@
+package org.apache.ctakes.ytex.ws;
+
+import java.util.List;
+
+import javax.jws.WebMethod;
+import javax.jws.WebService;
+
+import org.apache.ctakes.ytex.kernel.metric.ConceptPair;
+import org.apache.ctakes.ytex.kernel.metric.ConceptPairSimilarity;
+
+@WebService
+public interface ConceptSimilarityWebService {
+	public SimServiceInfo getDefaultConceptGraph();
+
+	public List<SimServiceInfo> getConceptGraphs();
+
+	/**
+	 * compute similarity for a list of concept pairs
+	 * 
+	 * @param conceptGraphName optional
+	 * @param conceptPairs
+	 *            required, concept pairs for which similarity should be
+	 *            computed
+	 * @param metrics
+	 *            required, similarity metrics to compute
+	 * @param lcs
+	 *            optional - if true, fill in the lcs paths for each concept pair.
+	 * @return similarities
+	 */
+	@WebMethod
+	public List<ConceptPairSimilarity> similarities(String conceptGraph,
+			ConceptPair[] conceptPairs, String[] metrics, boolean lcs);
+}

Added: ctakes/branches/ytex/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/ConceptSimilarityWebServiceImpl.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/ConceptSimilarityWebServiceImpl.java?rev=1560995&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/ConceptSimilarityWebServiceImpl.java (added)
+++ ctakes/branches/ytex/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/ConceptSimilarityWebServiceImpl.java Fri Jan 24 13:33:09 2014
@@ -0,0 +1,99 @@
+package org.apache.ctakes.ytex.ws;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.jws.WebService;
+import javax.ws.rs.WebApplicationException;
+
+import org.apache.ctakes.ytex.kernel.metric.ConceptPair;
+import org.apache.ctakes.ytex.kernel.metric.ConceptPairSimilarity;
+import org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService;
+import org.apache.ctakes.ytex.kernel.metric.LCSPath;
+import org.apache.ctakes.ytex.kernel.metric.SimilarityInfo;
+import org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService.SimilarityMetricEnum;
+import org.apache.ctakes.ytex.web.search.SemanticSimRegistryBean;
+
+@WebService(endpointInterface = "org.apache.ctakes.ytex.ws.ConceptSimilarityWebService")
+public class ConceptSimilarityWebServiceImpl implements
+		ConceptSimilarityWebService, ConceptSimilarityRestService {
+	public SemanticSimRegistryBean getSemanticSimRegistryBean() {
+		return semanticSimRegistryBean;
+	}
+
+	public void setSemanticSimRegistryBean(
+			SemanticSimRegistryBean semanticSimRegistryBean) {
+		this.semanticSimRegistryBean = semanticSimRegistryBean;
+	}
+
+	SemanticSimRegistryBean semanticSimRegistryBean;
+
+	public ConceptPairSimilarity similarity(String conceptGraph,
+			String concept1, String concept2, String metrics, String lcs) {
+		ConceptSimilarityService s = getConceptSimilarityService(conceptGraph);
+		if (s == null)
+			return null;
+		List<SimilarityMetricEnum> metricList = this
+				.metricArrayToList(metrics.split(","));
+		if (metricList.size() == 0)
+			return null;
+		return s.similarity(metricList, concept1, concept2, null,
+				"true".equalsIgnoreCase(lcs));
+	}
+
+	private ConceptSimilarityService getConceptSimilarityService(
+			String conceptGraph) {
+		String conceptGraphName = conceptGraph;
+		if (conceptGraphName == null || conceptGraphName.length() == 0)
+			conceptGraphName = semanticSimRegistryBean
+					.getDefaultConceptGraphName();
+		ConceptSimilarityService s = semanticSimRegistryBean
+				.getSemanticSimServiceMap().get(conceptGraphName)
+				.getConceptSimilarityService();
+		return s;
+	}
+
+	public List<ConceptPairSimilarity> similarities(String conceptGraph,
+			ConceptPair[] conceptPairs, String[] metrics, boolean lcs) {
+		ConceptSimilarityService s = this
+				.getConceptSimilarityService(conceptGraph);
+		List<SimilarityMetricEnum> metricList = metricArrayToList(metrics);
+		List<ConceptPair> conceptPairList = Arrays.asList(conceptPairs);
+		return s.similarity(conceptPairList, metricList, null, lcs);
+	}
+
+	private List<SimilarityMetricEnum> metricArrayToList(String[] metrics) {
+		List<SimilarityMetricEnum> metricIndexMap = new ArrayList<SimilarityMetricEnum>();
+		for (String metric : metrics) {
+			SimilarityMetricEnum m = SimilarityMetricEnum.valueOf(metric);
+			if (m != null)
+				metricIndexMap.add(m);
+		}
+		return metricIndexMap;
+	}
+
+	public SimServiceInfo getDefaultConceptGraph() {
+		String conceptGraph = this.semanticSimRegistryBean
+				.getDefaultConceptGraphName();
+		if (conceptGraph != null)
+			return new SimServiceInfo(conceptGraph, semanticSimRegistryBean
+					.getSemanticSimServiceMap().get(conceptGraph)
+					.getDescription());
+		else
+			return null;
+	}
+
+	public List<SimServiceInfo> getConceptGraphs() {
+		List<SimServiceInfo> cgs = new ArrayList<SimServiceInfo>(
+				semanticSimRegistryBean.getSemanticSimDescriptionMap().size());
+		for (Map.Entry<String, String> entry : semanticSimRegistryBean
+				.getSemanticSimDescriptionMap().entrySet()) {
+			cgs.add(new SimServiceInfo(entry.getValue(), entry.getKey()));
+		}
+		return cgs;
+	}
+
+}

Added: ctakes/branches/ytex/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/SimServiceInfo.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/SimServiceInfo.java?rev=1560995&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/SimServiceInfo.java (added)
+++ ctakes/branches/ytex/ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/SimServiceInfo.java Fri Jan 24 13:33:09 2014
@@ -0,0 +1,30 @@
+package org.apache.ctakes.ytex.ws;
+
+import javax.xml.bind.annotation.XmlRootElement;
+
+@XmlRootElement(name = "simServiceInfo")
+public class SimServiceInfo {
+	String conceptGraph;
+	String description;
+	public String getConceptGraph() {
+		return conceptGraph;
+	}
+	public void setConceptGraph(String conceptGraph) {
+		this.conceptGraph = conceptGraph;
+	}
+	public String getDescription() {
+		return description;
+	}
+	public void setDescription(String description) {
+		this.description = description;
+	}
+	public SimServiceInfo() {
+		super();
+	}
+	public SimServiceInfo(String conceptGraph, String description) {
+		super();
+		this.conceptGraph = conceptGraph;
+		this.description = description;
+	}
+
+}

Added: ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/applicationContext.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/applicationContext.xml?rev=1560995&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/applicationContext.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/applicationContext.xml Fri Jan 24 13:33:09 2014
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE beans PUBLIC "-//SPRING//DTD BEAN//EN" "http://www.springframework.org/dtd/spring-beans.dtd">
+<beans>
+	<import resource="classpath:/org/apache/ctakes/ytex/beans-datasource.xml" />
+	<import resource="classpath:/org/apache/ctakes/ytex/beans-kernel.hbm.xml" />
+	<import resource="classpath:/org/apache/ctakes/ytex/beans-kernel.xml" />
+	<import resource="classpath:/org/apache/ctakes/ytex/web/beans-kernel-simweb.xml" />
+	<import resource="classpath:/org/apache/ctakes/ytex/web/beans-web.xml" />
+	<import resource="classpath:/org/apache/ctakes/ytex/web/beans-ws.xml" />
+</beans>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/faces-config.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/faces-config.xml?rev=1560995&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/faces-config.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/faces-config.xml Fri Jan 24 13:33:09 2014
@@ -0,0 +1,90 @@
+<faces-config xmlns="http://java.sun.com/xml/ns/javaee"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://java.sun.com/xml/ns/javaee/web-facesconfig_2_0.xsd"
+	version="2.0">
+	<application>
+		<variable-resolver>org.springframework.web.jsf.DelegatingVariableResolver
+		</variable-resolver>
+		<locale-config>
+			<default-locale>en_US</default-locale>
+		</locale-config>
+		<resource-bundle>
+			<base-name>org.apache.ctakes.ytex.web.messages</base-name>
+			<var>msg</var>
+		</resource-bundle>
+	</application>
+
+	<managed-bean>
+		<managed-bean-name>semanticSearchBean</managed-bean-name>
+		<managed-bean-class>org.apache.ctakes.ytex.web.search.SemanticSearchBean
+		</managed-bean-class>
+		<managed-bean-scope>session</managed-bean-scope>
+		<managed-property>
+			<property-name>umlsFirstWordService</property-name>
+			<value>#{umlsFirstWordService}</value>
+		</managed-property>
+		<managed-property>
+			<property-name>documentSearchService</property-name>
+			<value>#{documentSearchService}</value>
+		</managed-property>
+	</managed-bean>
+	<managed-bean>
+		<managed-bean-name>documentViewBean</managed-bean-name>
+		<managed-bean-class>org.apache.ctakes.ytex.web.search.DocumentViewBean
+		</managed-bean-class>
+		<managed-bean-scope>view</managed-bean-scope>
+		<managed-property>
+			<property-name>dataSource</property-name>
+			<property-class></property-class>
+			<value>#{dataSource}</value>
+		</managed-property>
+		<managed-property>
+			<property-name>searchProperties</property-name>
+			<property-class></property-class>
+			<value>#{searchProperties}</value>
+		</managed-property>
+		<managed-property>
+			<property-name>ytexProperties</property-name>
+			<property-class></property-class>
+			<value>#{ytexProperties}</value>
+		</managed-property>		
+	</managed-bean>
+	<managed-bean>
+		<managed-bean-name>concept1</managed-bean-name>
+		<managed-bean-class>org.apache.ctakes.ytex.web.search.ConceptLookupBean
+		</managed-bean-class>
+		<managed-bean-scope>session</managed-bean-scope>
+		<managed-property>
+			<property-name>umlsFirstWordService</property-name>
+			<value>#{umlsFirstWordService}</value>
+		</managed-property>
+	</managed-bean>
+	<managed-bean>
+		<managed-bean-name>concept2</managed-bean-name>
+		<managed-bean-class>org.apache.ctakes.ytex.web.search.ConceptLookupBean
+		</managed-bean-class>
+		<managed-bean-scope>session</managed-bean-scope>
+		<managed-property>
+			<property-name>umlsFirstWordService</property-name>
+			<value>#{umlsFirstWordService}</value>
+		</managed-property>
+	</managed-bean>
+	<managed-bean>
+		<managed-bean-name>semanticSimBean</managed-bean-name>
+		<managed-bean-class>org.apache.ctakes.ytex.web.search.SemanticSimBean
+		</managed-bean-class>
+		<managed-bean-scope>session</managed-bean-scope>
+		<managed-property>
+			<property-name>concept1</property-name>
+			<value>#{concept1}</value>
+		</managed-property>
+		<managed-property>
+			<property-name>concept2</property-name>
+			<value>#{concept2}</value>
+		</managed-property>
+		<managed-property>
+			<property-name>semanticSimRegistryBean</property-name>
+			<value>#{semanticSimRegistryBean}</value>
+		</managed-property>
+	</managed-bean>
+</faces-config>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/inc-content/header.xhtml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/inc-content/header.xhtml?rev=1560995&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/inc-content/header.xhtml (added)
+++ ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/inc-content/header.xhtml Fri Jan 24 13:33:09 2014
@@ -0,0 +1,28 @@
+<div xmlns="http://www.w3.org/1999/xhtml"
+	xmlns:ice="http://www.icesoft.com/icefaces/component">
+	<div id="banner">
+		<table>
+			<tr>
+				<td><img src="images/ysm_home_banner.gif" height="60" />
+				</td>
+				<td>#{contentHeader}</td>
+			</tr>
+		</table>
+	</div>
+
+	<div id="mainNav">
+		<ice:form>
+			<ice:menuBar>
+				<ice:menuItem id="semanticSearchMenuItem" value="Semantic Search"
+					link="./semanticSearch.iface" />
+				<ice:menuItem id="semanticSimMenuItem" value="Semantic Similarity - Single"
+					link="./semanticSim.iface" />
+				<ice:menuItem id="semanticSimMultiMenuItem" value="Semantic Similarity - Multi"
+					link="./semanticSimMulti.iface" />
+				<ice:menuItem id="aboutMenuItem" value="About" link="./about.iface" />
+			</ice:menuBar>
+		</ice:form>
+	</div>
+	<div id="mainNavSpace"></div>
+
+</div>

Added: ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/inc-templates/commonLayout.xhtml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/inc-templates/commonLayout.xhtml?rev=1560995&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/inc-templates/commonLayout.xhtml (added)
+++ ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/inc-templates/commonLayout.xhtml Fri Jan 24 13:33:09 2014
@@ -0,0 +1,35 @@
+<?xml version='1.0' encoding='UTF-8' ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml"
+	xmlns:ui="http://java.sun.com/jsf/facelets"
+	xmlns:f="http://java.sun.com/jsf/core"
+	xmlns:h="http://java.sun.com/jsf/html"
+	xmlns:icecore="http://www.icefaces.org/icefaces/core"
+	xmlns:ace="http://www.icefaces.org/icefaces/components"
+	xmlns:ice="http://www.icesoft.com/icefaces/component">
+<h:head>
+	<title>YTEX - #{pageTitle}</title>
+	<link href="./xmlhttp/css/xp/xp.css" rel="stylesheet" type="text/css" />
+	<!-- page title param passed in by param -->
+	<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+	<meta http-equiv="Content-Language" content="en" />
+	<meta http-equiv="imagetoolbar" content="no" />
+	<meta name="keywords" content="" />
+	<meta name="description" content="" />
+	<link type="text/css" rel="stylesheet" href="css/mainscript.css" />
+	<!-- -->
+	<!-- override styles in xp.css here -->
+	<link href="css/menuStyle.css" rel="stylesheet" type="text/css" />
+	<link type="image/x-icon" rel="shortcut icon" href="images/favicon.ico" />
+</h:head>
+<h:body>
+	<div class="header">
+		<ui:include src="/WEB-INF/inc-content/header.xhtml" />
+	</div>
+
+	<div class="page-container-header">
+		<ui:insert name="pageContent" />
+	</div>
+
+</h:body>
+</html>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/web.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/web.xml?rev=1560995&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/web.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/WEB-INF/web.xml Fri Jan 24 13:33:09 2014
@@ -0,0 +1,87 @@
+<web-app>
+
+	<context-param>
+		<param-name>com.icesoft.faces.debugDOMUpdate</param-name>
+		<param-value>false</param-value>
+	</context-param>
+
+	<context-param>
+		<param-name>javax.faces.STATE_SAVING_METHOD</param-name>
+		<param-value>server</param-value>
+		<description>
+			State saving method: "client" or "server" (= default)
+			See
+			JSF Specification 2.5.2
+        </description>
+	</context-param>
+
+	<context-param>
+		<param-name>com.icesoft.faces.concurrentDOMViews</param-name>
+		<param-value>true</param-value>
+	</context-param>
+
+	<context-param>
+		<param-name>com.icesoft.faces.synchronousUpdate</param-name>
+		<param-value>true</param-value>
+	</context-param>
+
+	<context-param>
+		<param-name>contextConfigLocation</param-name>
+		<param-value>/WEB-INF/applicationContext.xml</param-value>
+	</context-param>
+	<listener>
+		<listener-class>org.springframework.web.context.ContextLoaderListener</listener-class>
+	</listener>
+	<listener>
+		<listener-class>org.springframework.web.context.request.RequestContextListener</listener-class>
+	</listener>
+	<listener>
+		<listener-class>com.sun.faces.config.ConfigureListener</listener-class>
+	</listener>
+	<!-- Faces Servlet -->
+	<servlet>
+		<servlet-name>Faces Servlet</servlet-name>
+		<servlet-class>javax.faces.webapp.FacesServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+	<servlet>
+		<servlet-name>Resource Servlet</servlet-name>
+		<servlet-class>com.icesoft.faces.webapp.CompatResourceServlet
+		</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+	<servlet>
+		<servlet-name>CXFServlet</servlet-name>
+		<display-name>CXF Servlet</display-name>
+		<servlet-class>org.apache.cxf.transport.servlet.CXFServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+	<!-- extension mapping -->
+	<servlet-mapping>
+		<servlet-name>Faces Servlet</servlet-name>
+		<url-pattern>*.jsf</url-pattern>
+		<url-pattern>*.iface</url-pattern>
+		<url-pattern>/icefaces/*</url-pattern>
+	</servlet-mapping>
+	<servlet-mapping>
+		<servlet-name>Resource Servlet</servlet-name>
+		<url-pattern>/xmlhttp/*</url-pattern>
+		<url-pattern>/resources/*</url-pattern>
+	</servlet-mapping>
+	<servlet-mapping>
+		<servlet-name>CXFServlet</servlet-name>
+		<url-pattern>/services/*</url-pattern>
+	</servlet-mapping>
+		
+	<session-config>
+		<session-timeout>5</session-timeout>
+	</session-config>
+
+	<!-- Welcome files -->
+	<welcome-file-list>
+		<welcome-file>index.jsf</welcome-file>
+		<welcome-file>index.jsp</welcome-file>
+		<welcome-file>index.html</welcome-file>
+	</welcome-file-list>
+
+</web-app>
\ No newline at end of file

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URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/about.xhtml?rev=1560995&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/about.xhtml (added)
+++ ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/about.xhtml Fri Jan 24 13:33:09 2014
@@ -0,0 +1,36 @@
+<?xml version='1.0' encoding='UTF-8' ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml"
+	xmlns:ui="http://java.sun.com/jsf/facelets"
+	xmlns:f="http://java.sun.com/jsf/core"
+	xmlns:h="http://java.sun.com/jsf/html"
+	xmlns:icecore="http://www.icefaces.org/icefaces/core"
+	xmlns:ace="http://www.icefaces.org/icefaces/components"
+	xmlns:ice="http://www.icesoft.com/icefaces/component">
+
+<h:body>
+	<ui:composition template="WEB-INF/inc-templates/commonLayout.xhtml">
+		<!-- params for page titles-->
+		<ui:param name="pageTitle" value="About" />
+		<ui:param name="contentHeader" value="About YTEX" />
+
+		<!-- header content here  -->
+		<ui:define name="pageName">
+                #{contentHeader}
+        </ui:define>
+
+		<!-- insert content here -->
+		<ui:define name="pageContent">
+			<div id="docText">
+				YTEX - Yale cTAKES Extensions. Refer to the <a
+					href="http://code.google.com/p/ytex/">YTEX home page</a> for more
+				information.
+			</div>
+		</ui:define>
+
+
+	</ui:composition>
+
+</h:body>
+
+</html>
\ No newline at end of file

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--- ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/css/mainscript.css (added)
+++ ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/css/mainscript.css Fri Jan 24 13:33:09 2014
@@ -0,0 +1,44 @@
+#banner	
+{
+	background-color: #0e4d94;
+	border-bottom: 1px solid #fff;
+	width: 100%;
+	color: white;
+	padding-left: 10px;
+	font-size: 38px;
+	vertical-align: middle
+}
+
+#banner	table
+{
+	border: 0px;
+	color: white;
+	font-family: Georgia, "Times New Roman", Times, serif;
+}
+	
+
+
+#mainNav
+{
+	width: 100%;
+	background-color: #c7511f;
+	height: 25px
+}
+
+#mainNavSpace
+{
+	width: 100%;
+	height: 10px
+}
+
+
+body {
+    margin: 0;
+    padding: 0;
+}
+
+
+#docText {
+	padding-left: 10px;
+}
+

Added: ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/css/menuStyle.css
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/css/menuStyle.css?rev=1560995&view=auto
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--- ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/css/menuStyle.css (added)
+++ ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/css/menuStyle.css Fri Jan 24 13:33:09 2014
@@ -0,0 +1,32 @@
+.iceMnuBar { 
+    background-color: #C7511F;
+	padding: 0px;
+    white-space: nowrap;
+    font-family: Verdana, Arial, Helvetica, sans-serif;
+    width: 100%;
+    padding: 0px;
+}
+
+.iceMnuBarItem { 
+    padding: 0px;
+    white-space: nowrap;
+    float: none;
+}
+.iceMnuBarItem a { 
+    background-color: #C7511F;
+    height: auto;
+    padding-left: 10px;
+    padding-right: 10px;
+    padding-top: 3px;
+    padding-bottom: 3px;
+	color: #fff;
+    margin: 0px;
+    border-right: 1px solid #FFFFFF;
+    width: auto;
+    display: block;
+    text-decoration: none;
+}
+.iceMnuBarItem a:hover { 
+	background-color: #C7511F;
+	color: #fe6;
+}

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--- ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/index.jsp (added)
+++ ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/index.jsp Fri Jan 24 13:33:09 2014
@@ -0,0 +1,11 @@
+<%-- 
+<%
+response.sendRedirect("semanticSearch.jsf");
+%>
+--%>
+<html>
+    <head> </head>
+    <body>
+        <jsp:forward page="semanticSim.jsf" />
+    </body>
+</html>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/metricCheckboxes.xhtml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/metricCheckboxes.xhtml?rev=1560995&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/metricCheckboxes.xhtml (added)
+++ ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/metricCheckboxes.xhtml Fri Jan 24 13:33:09 2014
@@ -0,0 +1,41 @@
+<div xmlns="http://www.w3.org/1999/xhtml"
+	xmlns:f="http://java.sun.com/jsf/core"
+	xmlns:h="http://java.sun.com/jsf/html"
+	xmlns:ice="http://www.icesoft.com/icefaces/component">
+	<table>
+		<tr>
+			<th align="left">Path Finding</th>
+			<th align="left">Intrinsic InfoContent</th>
+			<th align="left">Corpus InfoContent</th>
+		</tr>
+		<tr>
+			<td valign="top"><h:selectManyCheckbox
+					value="#{semanticSimBean.metricSelectTaxonomy}"
+					layout="pageDirection">
+					<f:selectItem itemValue="WUPALMER" itemLabel="Wu-Palmer" />
+					<f:selectItem itemValue="PATH" itemLabel="Path" />
+					<f:selectItem itemValue="LCH" itemLabel="Leacock &amp; Chodorow" />
+					<f:selectItem itemValue="RADA" itemLabel="Rada" />
+				</h:selectManyCheckbox>
+			</td>
+			<td valign="top"><h:selectManyCheckbox
+					value="#{semanticSimBean.metricSelectIntrinsicIC}"
+					layout="pageDirection">
+					<f:selectItem itemValue="INTRINSIC_LIN" itemLabel="Lin" />
+					<f:selectItem itemValue="INTRINSIC_PATH" itemLabel="Path" />
+					<f:selectItem itemValue="INTRINSIC_LCH"
+						itemLabel="Leacock &amp; Chodorow" />
+					<f:selectItem itemValue="INTRINSIC_RADA" itemLabel="Rada" />
+					<f:selectItem itemValue="JACCARD" itemLabel="Jaccard" />
+					<f:selectItem itemValue="SOKAL" itemLabel="Sokal &amp; Sneath" />
+				</h:selectManyCheckbox>
+			</td>
+			<td valign="top"><h:selectManyCheckbox
+					value="#{semanticSimBean.metricSelectCorpusIC}"
+					layout="pageDirection">
+					<f:selectItem itemValue="LIN" itemLabel="Lin" />
+				</h:selectManyCheckbox>
+			</td>
+		</tr>
+	</table>
+</div>

Added: ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/semanticSearch.xhtml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/semanticSearch.xhtml?rev=1560995&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/semanticSearch.xhtml (added)
+++ ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/semanticSearch.xhtml Fri Jan 24 13:33:09 2014
@@ -0,0 +1,156 @@
+<?xml version='1.0' encoding='UTF-8' ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml"
+	xmlns:ui="http://java.sun.com/jsf/facelets"
+	xmlns:f="http://java.sun.com/jsf/core"
+	xmlns:h="http://java.sun.com/jsf/html"
+	xmlns:icecore="http://www.icefaces.org/icefaces/core"
+	xmlns:ace="http://www.icefaces.org/icefaces/components"
+	xmlns:ice="http://www.icesoft.com/icefaces/component">
+
+<h:body>
+	<ui:composition template="WEB-INF/inc-templates/commonLayout.xhtml">
+		<!-- params for page titles-->
+		<ui:param name="pageTitle" value="Semantic Search" />
+		<ui:param name="contentHeader" value="Semantic Search" />
+
+		<!-- header content here  -->
+		<ui:define name="pageName">
+                #{contentHeader}
+        </ui:define>
+
+		<!-- insert content here -->
+		<ui:define name="pageContent">
+			<ice:form id="umlsSearch">
+				<ice:panelGrid columns="1">
+					<ice:panelGroup>
+						<table border="0">
+							<tr valign="top">
+								<td><ice:outputLabel id="codeLabel" value="Concept ID:" />
+								</td>
+								<td><ice:outputText
+										value="Enter the first word of the concept and select a concept ID" /><br />
+									<ice:selectInputText id="codeInput" rows="30" width="300"
+										valueChangeListener="#{semanticSearchBean.updateList}"
+										required="true">
+										<f:selectItems value="#{semanticSearchBean.list}" />
+									</ice:selectInputText></td>
+							</tr>
+							<tr valign="top">
+								<td><ice:outputLabel id="patientIdLabel"
+										value="Patient ID:" /></td>
+								<td><ice:inputText id="patientIdInput"
+										value="#{semanticSearchBean.patientId}" required="false">
+										<f:convertNumber integerOnly="true" groupingUsed="false" />
+									</ice:inputText></td>
+							</tr>
+							<tr valign="top">
+								<td><ice:outputLabel id="fromDateTxt" value="From Date:" />
+								</td>
+								<td><ice:selectInputDate id="fromDateInput"
+										renderMonthAsDropdown="true" renderYearAsDropdown="true"
+										value="#{semanticSearchBean.dateFrom}" title="From Date"
+										renderAsPopup="true" required="false">
+										<f:convertDateTime pattern="MM/dd/yyyy" />
+									</ice:selectInputDate></td>
+							</tr>
+							<tr valign="top">
+								<td><ice:outputLabel id="toDateTxt" value="To Date:" /></td>
+								<td><ice:selectInputDate id="toDateInput"
+										renderMonthAsDropdown="true" renderYearAsDropdown="true"
+										value="#{semanticSearchBean.dateTo}" title="To Date"
+										renderAsPopup="true" required="false">
+										<f:convertDateTime pattern="MM/dd/yyyy" />
+									</ice:selectInputDate></td>
+							</tr>
+							<tr valign="top">
+								<td><ice:outputLabel id="negationContextLabel"
+										value="Negation Context:" /></td>
+								<td><ice:selectOneRadio id="negationContextInput"
+										value="#{semanticSearchBean.negationStatus}" required="false">
+										<f:selectItem itemValue="#{true}" itemLabel="Affirmed" />
+										<f:selectItem itemValue="#{false}" itemLabel="Negated" />
+									</ice:selectOneRadio></td>
+							</tr>
+						</table>
+						<ice:commandButton id="Search" value="Search" title="Search"
+							actionListener="#{semanticSearchBean.searchListen}" />
+						<ice:commandButton id="Reset" value="Reset" title="Reset"
+							actionListener="#{semanticSearchBean.resetListen}" />
+					</ice:panelGroup>
+					<br />
+					<ice:panelGroup>
+						<ice:outputText value="Search Term:" style="font-weight:bold;" />
+						<ice:panelGrid columns="2">
+							<ice:outputText value="CUI:" />
+							<ice:outputText id="cui"
+								value="#{semanticSearchBean.searchCUI.conceptId}" />
+							<ice:outputText value="Text:" />
+							<ice:outputText id="text"
+								value="#{semanticSearchBean.searchCUI.text}" />
+						</ice:panelGrid>
+					</ice:panelGroup>
+
+				</ice:panelGrid>
+			</ice:form>
+
+
+			<ice:form>
+				<ice:dataTable value="#{semanticSearchBean.searchResultList}"
+					var="item">
+
+					<ice:column>
+						<f:facet name="header">
+							<ice:outputText value="Doc ID" />
+						</f:facet>
+						<ice:outputLink
+							value="./viewDocument.iface?documentID=#{item.documentID}">
+							<ice:outputText value="#{item.documentID}" />
+						</ice:outputLink>
+					</ice:column>
+
+					<ice:column>
+						<f:facet name="header">
+							<ice:outputText value="Date" />
+						</f:facet>
+						<ice:outputText value="#{item.documentDate}" />
+					</ice:column>
+
+					<ice:column>
+						<f:facet name="header">
+							<ice:outputText value="Title" />
+						</f:facet>
+						<ice:outputText value="#{item.documentTitle}" />
+					</ice:column>
+
+					<ice:column>
+						<f:facet name="header">
+							<ice:outputText value="Doc Type" />
+						</f:facet>
+						<ice:outputText value="#{item.documentTypeName}" />
+					</ice:column>
+
+					<ice:column>
+						<f:facet name="header">
+							<ice:outputText value="Term" />
+						</f:facet>
+						<ice:outputText value="#{item.cuiText}" />
+					</ice:column>
+
+					<ice:column>
+						<f:facet name="header">
+							<ice:outputText value="Sentence" />
+						</f:facet>
+						<ice:outputText value="#{item.sentenceText}" />
+					</ice:column>
+
+				</ice:dataTable>
+			</ice:form>
+		</ui:define>
+
+
+	</ui:composition>
+
+</h:body>
+
+</html>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/semanticSim.xhtml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/semanticSim.xhtml?rev=1560995&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/semanticSim.xhtml (added)
+++ ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/semanticSim.xhtml Fri Jan 24 13:33:09 2014
@@ -0,0 +1,142 @@
+<?xml version='1.0' encoding='UTF-8' ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml"
+	xmlns:ui="http://java.sun.com/jsf/facelets"
+	xmlns:f="http://java.sun.com/jsf/core"
+	xmlns:h="http://java.sun.com/jsf/html"
+	xmlns:c="http://java.sun.com/jstl/core"
+	xmlns:icecore="http://www.icefaces.org/icefaces/core"
+	xmlns:ace="http://www.icefaces.org/icefaces/components"
+	xmlns:ice="http://www.icesoft.com/icefaces/component">
+
+<h:body>
+	<ui:composition template="WEB-INF/inc-templates/commonLayout.xhtml">
+		<!-- params for page titles-->
+		<ui:param name="pageTitle" value="Semantic Similarity" />
+		<ui:param name="contentHeader" value="Semantic Similarity" />
+
+		<!-- header content here  -->
+		<ui:define name="pageName">
+                #{contentHeader}
+        </ui:define>
+
+		<!-- insert content here -->
+		<ui:define name="pageContent">
+			<ice:form id="conceptGraphFrom">
+				<ice:panelGrid columns="1">
+					<ice:panelGroup>
+						<table border="0">
+							<tr valign="top">
+								<td><ice:outputLabel id="conceptGraphLabel"
+										value="Concept Graph:" /></td>
+								<td><ice:selectOneMenu
+										value="#{semanticSimBean.conceptGraphName}"
+										valueChangeListener="#{semanticSimBean.updateConceptGraph}"
+										partialSubmit="true">
+										<f:selectItems
+											value="#{semanticSimBean.semanticSimRegistryBean.semanticSimDescriptionMap}" />
+									</ice:selectOneMenu></td>
+							</tr>
+						</table>
+					</ice:panelGroup>
+				</ice:panelGrid>
+			</ice:form>
+			<ice:form id="umlsSearch">
+				<ice:panelGrid columns="1">
+					<ice:panelGroup>
+						<table border="0">
+							<tr valign="top">
+								<td><ice:outputLabel id="codeLabel1" value="Concept 1:" />
+								</td>
+								<td><ice:selectInputText id="codeInput1" rows="30"
+										width="300"
+										valueChangeListener="#{semanticSimBean.concept1.updateList}"
+										required="true">
+										<f:selectItems value="#{semanticSimBean.concept1.list}" />
+									</ice:selectInputText>
+								</td>
+							</tr>
+							<tr valign="top">
+								<td><ice:outputLabel id="codeLabel2" value="Concept 2:" />
+								</td>
+								<td><ice:selectInputText id="codeInput2" rows="30"
+										width="300"
+										valueChangeListener="#{semanticSimBean.concept2.updateList}"
+										required="true">
+										<f:selectItems value="#{semanticSimBean.concept2.list}" />
+									</ice:selectInputText>
+								</td>
+							</tr>
+							<tr>
+								<td valign="top">Metrics:</td>
+								<td><ui:include src="metricCheckboxes.xhtml" /></td>
+							</tr>
+						</table>
+						<ice:commandButton id="Similarity" value="Similarity"
+							title="ComputeSimilarity"
+							actionListener="#{semanticSimBean.simListen}" />
+						<ice:commandButton id="Reset" value="Reset" title="Reset"
+							actionListener="#{semanticSimBean.resetListen}" />
+					</ice:panelGroup>
+				</ice:panelGrid>
+			</ice:form>
+			<ice:form>
+				<ice:outputText
+					value="Concept 1: #{semanticSimBean.concept1.searchCUI.text} [#{semanticSimBean.concept1.searchCUI.conceptId}]" />
+				<br />
+				<ice:outputText
+					value="Concept 2: #{semanticSimBean.concept2.searchCUI.text} [#{semanticSimBean.concept2.searchCUI.conceptId}]" />
+				<!-- similarity for each metric -->
+				<ice:dataTable value="#{semanticSimBean.similarityMap}" var="entry">
+					<ice:column>
+						<f:facet name="header">
+							<ice:outputText value="Metric" />
+						</f:facet>
+						<ice:outputText value="#{msg[entry.key]}" />
+					</ice:column>
+					<ice:column>
+						<f:facet name="header">
+							<ice:outputText value="Similarity" />
+						</f:facet>
+						<ice:outputText value="#{entry.value}">
+							<f:convertNumber maxFractionDigits="4" minFractionDigits="4" />
+						</ice:outputText>
+					</ice:column>
+				</ice:dataTable>
+				<c:if test="${!empty semanticSimBean.simInfo.corpusLcs}">
+					<br />
+					<ice:outputText
+						value="Corpus LCS: #{semanticSimBean.corpusLcsTerm} [#{semanticSimBean.simInfo.corpusLcs}]" />
+				</c:if>
+				<c:if test="${!empty semanticSimBean.simInfo.intrinsicLcs}">
+					<br />
+					<ice:outputText
+						value="Intrinsic LCS: #{semanticSimBean.intrinsicLcsTerm} [#{semanticSimBean.simInfo.intrinsicLcs}]" />
+				</c:if>
+				<c:if test="${!empty semanticSimBean.lcsPathMap}">
+					<br />
+					<!-- detailed lcs info -->
+					<ice:dataTable value="#{semanticSimBean.lcsPathMap}" var="lcsEntry">
+						<ice:column>
+							<f:facet name="header">
+								<ice:outputText value="LCS" />
+							</f:facet>
+							<ice:outputText value="#{lcsEntry.key}" />
+						</ice:column>
+						<ice:column>
+							<f:facet name="header">
+								<ice:outputText value="Path" />
+							</f:facet>
+							<ice:outputText value="#{lcsEntry.value}" />
+						</ice:column>
+					</ice:dataTable>
+				</c:if>
+			</ice:form>
+		</ui:define>
+
+
+	</ui:composition>
+
+</h:body>
+
+</html>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/semanticSimMulti.xhtml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/semanticSimMulti.xhtml?rev=1560995&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/semanticSimMulti.xhtml (added)
+++ ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/semanticSimMulti.xhtml Fri Jan 24 13:33:09 2014
@@ -0,0 +1,104 @@
+<?xml version='1.0' encoding='UTF-8' ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml"
+	xmlns:ui="http://java.sun.com/jsf/facelets"
+	xmlns:f="http://java.sun.com/jsf/core"
+	xmlns:h="http://java.sun.com/jsf/html"
+	xmlns:c="http://java.sun.com/jstl/core"
+	xmlns:icecore="http://www.icefaces.org/icefaces/core"
+	xmlns:ace="http://www.icefaces.org/icefaces/components"
+	xmlns:ice="http://www.icesoft.com/icefaces/component">
+
+<h:body>
+	<ui:composition template="WEB-INF/inc-templates/commonLayout.xhtml">
+		<!-- params for page titles-->
+		<ui:param name="pageTitle" value="Semantic Similarity - Multi" />
+		<ui:param name="contentHeader" value="Semantic Similarity - Multi" />
+
+		<!-- header content here  -->
+		<ui:define name="pageName">
+                #{contentHeader}
+        </ui:define>
+
+		<!-- insert content here -->
+		<ui:define name="pageContent">
+			<ice:form id="conceptGraphFrom">
+				<ice:panelGrid columns="1">
+					<ice:panelGroup>
+						<table border="0">
+							<tr valign="top">
+								<td><ice:outputLabel id="conceptGraphLabel"
+									value="Concept Graph:" /></td>
+								<td><ice:selectOneMenu
+									value="#{semanticSimBean.conceptGraphName}"
+									valueChangeListener="#{semanticSimBean.updateConceptGraph}"
+									partialSubmit="true">
+									<f:selectItems
+										value="#{semanticSimBean.semanticSimRegistryBean.semanticSimDescriptionMap}" />
+								</ice:selectOneMenu></td>
+							</tr>
+						</table>
+					</ice:panelGroup>
+				</ice:panelGrid>
+			</ice:form>
+			<ice:form id="umlsSearch">
+				<ice:panelGrid columns="1">
+					<ice:panelGroup>
+						<table border="0">
+							<tr>
+								<td valign="top">Metrics:</td>
+								<td><ui:include src="metricCheckboxes.xhtml" /></td>
+							</tr>
+							<tr>
+								<td valign="top">Concept Pairs:</td>
+								<td><h:inputTextarea id="conceptPairText"
+									value="#{semanticSimBean.conceptPairText}"></h:inputTextarea></td>
+							</tr>
+						</table>
+						<ice:commandButton id="Similarity" value="Similarity"
+							title="ComputeSimilarity"
+							actionListener="#{semanticSimBean.simMultiListen}" />
+						<ice:commandButton id="Reset" value="Reset" title="Reset"
+							actionListener="#{semanticSimBean.resetListen}" />
+					</ice:panelGroup>
+				</ice:panelGrid>
+			</ice:form>
+			<ice:form>
+				<ice:dataExporter for="simTable" type="csv" label="Download as CSV" />
+				<ice:dataExporter for="simTable" type="excel"
+					label="Download as XLS" />
+				<!-- similarity for each metric -->
+				<ice:dataTable id="simTable"
+					value="#{semanticSimBean.similarityList}" var="entry">
+					<ice:column>
+						<f:facet name="header">
+							<ice:outputText value="Concept ID 1" />
+						</f:facet>
+						<ice:outputText value="#{entry.conceptPair.concept1}" />
+					</ice:column>
+					<ice:column>
+						<f:facet name="header">
+							<ice:outputText value="Concept ID 2" />
+						</f:facet>
+						<ice:outputText value="#{entry.conceptPair.concept2}" />
+					</ice:column>
+					<ice:columns value="#{semanticSimBean.metrics}" var="metric">
+						<f:facet name="header">
+							<ice:panelGroup>
+								<ice:outputText value="#{metric}" />
+							</ice:panelGroup>
+						</f:facet>
+						<!-- display the table cell values-->
+						<ice:panelGroup>
+							<ice:outputText value="#{entry.similarityMap[metric]}">
+								<f:convertNumber maxFractionDigits="4" minFractionDigits="4" />
+							</ice:outputText>
+						</ice:panelGroup>
+					</ice:columns>
+				</ice:dataTable>
+			</ice:form>
+		</ui:define>
+	</ui:composition>
+</h:body>
+
+</html>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/timeout.jsp
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/timeout.jsp?rev=1560995&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/timeout.jsp (added)
+++ ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/timeout.jsp Fri Jan 24 13:33:09 2014
@@ -0,0 +1,17 @@
+<%@page session="false"%>
+<%
+	String url = request.getRequestURL().substring(1,
+			request.getRequestURL().indexOf("/") + 1)
+			+ request.getContextPath();
+	response.sendRedirect(url);
+%>
+
+<html>
+<title>Session Timeout</title>
+<body>
+<h2>Invalid Session</h2>
+
+<p>Your session appears to have timed out. Please <a href="<%=url%>" />start
+again</a>.</p>
+</body>
+</html>

Added: ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/viewDocument.xhtml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/viewDocument.xhtml?rev=1560995&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/viewDocument.xhtml (added)
+++ ctakes/branches/ytex/ctakes-ytex-web/src/main/webapp/viewDocument.xhtml Fri Jan 24 13:33:09 2014
@@ -0,0 +1,36 @@
+<?xml version='1.0' encoding='UTF-8' ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml"
+	xmlns:ui="http://java.sun.com/jsf/facelets"
+	xmlns:f="http://java.sun.com/jsf/core"
+	xmlns:h="http://java.sun.com/jsf/html"
+	xmlns:icecore="http://www.icefaces.org/icefaces/core"
+	xmlns:ace="http://www.icefaces.org/icefaces/components"
+	xmlns:ice="http://www.icesoft.com/icefaces/component">
+
+<h:body>
+	<ui:composition template="WEB-INF/inc-templates/commonLayout.xhtml">
+		<!-- params for page titles-->
+		<ui:param name="pageTitle"
+			value="Document ID: #{documentViewBean.documentID}" />
+		<ui:param name="contentHeader"
+			value="Document ID: #{documentViewBean.documentID}" />
+
+		<!-- header content here  -->
+		<ui:define name="pageName">
+                #{contentHeader}
+        </ui:define>
+
+		<!-- insert content here -->
+		<ui:define name="pageContent">
+			<div id="docText">
+				<ice:outputText value="#{documentViewBean.docText}" escape="false" />
+			</div>
+		</ui:define>
+
+
+	</ui:composition>
+
+</h:body>
+
+</html>
\ No newline at end of file



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