o [GF#32685] Separate code from name in the simple search.

o	[GF#32711] Synchronize code and exactMatch radio buttons.
o	[GF#32730] Relabel roles and associations.
o	[GF#32731] Search NCIt only by default.
o	[GF#32737] Change charset from iso-8859-1 to UTF-8.
o	[GF#32746] Provide access to NCBO Bioportal ontology visualization widget
o	[GF#32772] Improve value set accessibility.
o	[GF#32779] Enhancement to Contains Search Functionality.
o	[GF#32790] Add an AnnotationProperty, Description, to Terminology_Value_Set.owl
o	[GF#32792] Make Advanced Search link more visible.
o	[GF#32793] Extend the advanced search capability.
o	[GF#32794] Implement value set entity search.
o	[GF#32811] Tagging of value sets.
o	[GF#32816] Migrate to LexEVSAPI 6.1.
o	[GF#32836] Allow the user to download the content of a mapping.
o	[GF#32769] Unable to render JSPs containing Chinese characters.
o	[GF#32870] Update the content of the NCI Thesaurus subset page.

software/build/build.xml

@@ -1,12 +1,5 @@
 <?xml version="1.0" encoding="utf-8" ?>
 
-<!--L
-  Copyright Northrop Grumman Information Technology.
-
-  Distributed under the OSI-approved BSD 3-Clause License.
-  See http://ncip.github.com/nci-term-browser/LICENSE.txt for details.
-L-->
-
 <project name="build" default="usage" basedir="." xmlns:bda="antlib:gov.nih.nci.bdalite">
 
     <description>
@@ -191,6 +184,7 @@ L-->
                 <filter token="ping.lexevs.enabled" value="${ping.lexevs.enabled}"/>
                 <filter token="ping.lexevs.interval" value="${ping.lexevs.interval}"/>
                 <filter token="audio_captcha_background_noise_on" value="${audio_captcha_background_noise_on}"/>
+                <filter token="ncbo_api_key" value="${ncbo_api_key}"/>
             </filterset>
             <resources>
                 <file file="${bda.conf.dir}/${webapp.prop.file}"/>

software/build/project.properties

@@ -1,10 +1,3 @@
-#L
-# Copyright Northrop Grumman Information Technology.
-#
-# Distributed under the OSI-approved BSD 3-Clause License.
-# See http://ncip.github.com/nci-term-browser/LICENSE.txt for details.
-#L
-
 ##############################################################
 #
 # BDA-Lite Project Property File
@@ -16,8 +9,8 @@
 ###  NCIT BROWSER SETTINGS (Defaults for the browser) ###
 #########################################################
 debug.on=false
-application.version=2.2
-application.version.display=Version $application.version (using LexEVS 6.0)
+application.version=2.3
+application.version.display=Version $application.version (using LexEVS 6.1)
 log.package=gov.nih.nci
 log.level=INFO
 ncitbrowser.conf.path=conf
@@ -53,13 +46,15 @@ jboss.server.inst=jboss-5.1.0.GA
 ##############################################################################
 ; application.data.path = Path used by application for cache and config files
 ; lex.evs.api.url = URL to the lexevsapi application (If "null", lg.config.file must point to a local lexevs instance)
+lex.evs.api.url=http://ncias-d499-v.nci.nih.gov:29780/lexevsapi61
 ; lg.config.file = Points to a local lexevs instance
 ; mail.smtp.server = Mail server to use for the 'Contact Us' page
 ; ncicb.contact.url = 'Contact Us' email address
 ; terminology.subset.download.url = URL to download page of NCI Report Writer application
 ; term.suggestion.application.url = URL to the NCI Suggest Term application
 ; ncit.url = URL to NCIt application
-; meddra_security_token = Medra security token
+; meddra_security_token = MedDRA security token
+; ncbo_api_key = NCBO API key
 ; license_page_option = Display license page flag
 ; audio_captcha_background_noise_on = Set to false to turn off the background noise for audio captcha (default to true)
 ;

software/ncitbrowser/conf/NCItBrowserProperties.xml

@@ -1,12 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
-<!--L
-  Copyright Northrop Grumman Information Technology.
-
-  Distributed under the OSI-approved BSD 3-Clause License.
-  See http://ncip.github.com/nci-term-browser/LICENSE.txt for details.
-L-->
-
 <root>
     <DisplayItems>
         <DisplayItem>
@@ -326,14 +319,6 @@ L-->
             <isExternalCode>true</isExternalCode>
        </DisplayItem>
 
-       <DisplayItem>
-            <propertyName>OMIM_Number</propertyName>
-            <itemLabel>OMIM Number</itemLabel>
-            <url>http://www.ncbi.nlm.nih.gov:80/entrez/dispomim.cgi?id=</url>
-            <hyperlinkText>see OMIM info</hyperlinkText>
-            <isExternalCode>true</isExternalCode>
-       </DisplayItem>
-
        <DisplayItem>
             <propertyName>PDQ_Closed_Trial_Search_ID</propertyName>
             <itemLabel>PDQ Closed Trial Search ID</itemLabel>
@@ -573,6 +558,11 @@ L-->
                  <key>AUDIO_CAPTCHA_BACKGROUND_NOISE_ON</key>
                  <value>@audio_captcha_background_noise_on@</value>
         </ConfigurableItem>
+
+        <ConfigurableItem>
+                 <key>NCBO_API_KEY</key>
+                 <value>@ncbo_api_key@</value>
+        </ConfigurableItem>
 
         <!-- Standard FTP Report List (End) ================================ -->
 

software/ncitbrowser/conf/application-config-client-info.xml

@@ -1,12 +1,4 @@
 <?xml version="1.0" encoding="UTF-8"?>
-
-<!--L
-  Copyright Northrop Grumman Information Technology.
-
-  Distributed under the OSI-approved BSD 3-Clause License.
-  See http://ncip.github.com/nci-term-browser/LICENSE.txt for details.
-L-->
-
 <!DOCTYPE beans PUBLIC "-//SPRING//DTD BEAN//EN" "http://www.springframework.org/dtd/spring-beans.dtd">
 <beans>
 

software/ncitbrowser/conf/application-config-client.xml

@@ -1,12 +1,4 @@
 <?xml version="1.0" encoding="UTF-8"?>
-
-<!--L
-  Copyright Northrop Grumman Information Technology.
-
-  Distributed under the OSI-approved BSD 3-Clause License.
-  See http://ncip.github.com/nci-term-browser/LICENSE.txt for details.
-L-->
-
 <!DOCTYPE beans PUBLIC "-//SPRING//DTD BEAN//EN" "http://www.springframework.org/dtd/spring-beans.dtd">
 <beans>
       <bean id="EvsServiceInfo" class="java.util.HashMap" singleton="false">

software/ncitbrowser/conf/ehcache.xml

@@ -1,10 +1,3 @@
-<!--L
-  Copyright Northrop Grumman Information Technology.
-
-  Distributed under the OSI-approved BSD 3-Clause License.
-  See http://ncip.github.com/nci-term-browser/LICENSE.txt for details.
-L-->
-
 <ehcache>
 <diskStore path="@ehcache.cache.path@"/>
 

software/ncitbrowser/conf/ncit-log4j.xml

@@ -1,12 +1,4 @@
 <?xml version="1.0" encoding="UTF-8" ?>
-
-<!--L
-  Copyright Northrop Grumman Information Technology.
-
-  Distributed under the OSI-approved BSD 3-Clause License.
-  See http://ncip.github.com/nci-term-browser/LICENSE.txt for details.
-L-->
-
 <!DOCTYPE log4j:configuration SYSTEM "@log4j.dtd.path@/log4j.dtd">
 
 <log4j:configuration xmlns:log4j='http://jakarta.apache.org/log4j/'>

software/ncitbrowser/src/java/gov/nih/nci/evs/browser/bean/CartActionBean.java

@@ -1,10 +1,3 @@
-/*L
- * Copyright Northrop Grumman Information Technology.
- *
- * Distributed under the OSI-approved BSD 3-Clause License.
- * See http://ncip.github.com/nci-term-browser/LICENSE.txt for details.
- */
-
 package gov.nih.nci.evs.browser.bean;
 
 import gov.nih.nci.evs.browser.utils.RemoteServerUtil;
@@ -27,7 +20,7 @@
 import org.LexGrid.LexBIG.DataModel.Collections.AbsoluteCodingSchemeVersionReferenceList;
 import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference;
 import org.LexGrid.LexBIG.Utility.Constructors;
-
+
 import javax.faces.component.html.HtmlSelectBooleanCheckbox;
 import javax.faces.context.FacesContext;
 import javax.servlet.http.HttpServletRequest;
@@ -57,7 +50,45 @@
 import gov.nih.nci.evs.browser.utils.*;
 
 /**
- * 
+ * <!-- LICENSE_TEXT_START -->
+ * Copyright 2008,2009 NGIT. This software was developed in conjunction
+ * with the National Cancer Institute, and so to the extent government
+ * employees are co-authors, any rights in such works shall be subject
+ * to Title 17 of the United States Code, section 105.
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *   1. Redistributions of source code must retain the above copyright
+ *      notice, this list of conditions and the disclaimer of Article 3,
+ *      below. Redistributions in binary form must reproduce the above
+ *      copyright notice, this list of conditions and the following
+ *      disclaimer in the documentation and/or other materials provided
+ *      with the distribution.
+ *   2. The end-user documentation included with the redistribution,
+ *      if any, must include the following acknowledgment:
+ *      "This product includes software developed by NGIT and the National
+ *      Cancer Institute."   If no such end-user documentation is to be
+ *      included, this acknowledgment shall appear in the software itself,
+ *      wherever such third-party acknowledgments normally appear.
+ *   3. The names "The National Cancer Institute", "NCI" and "NGIT" must
+ *      not be used to endorse or promote products derived from this software.
+ *   4. This license does not authorize the incorporation of this software
+ *      into any third party proprietary programs. This license does not
+ *      authorize the recipient to use any trademarks owned by either NCI
+ *      or NGIT
+ *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED
+ *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE
+ *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
+ *      NGIT, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT,
+ *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+ *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
+ *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ *      POSSIBILITY OF SUCH DAMAGE.
+ * <!-- LICENSE_TEXT_END -->
  */
 
 /**
@@ -220,8 +251,8 @@ public String addToCart() throws Exception {
         String name = null;
         String url = null;
         String version = null;
-        String type = null;
-
+        String type = null;
+
         _messageflag = false;
 
         // Get concept information from the Entity item passed in
@@ -289,7 +320,7 @@ public String addToCart() throws Exception {
         item.setUrl(url);
 
         if (!_cart.containsKey(code))
-        	_cart.put(code,item);
+        	_cart.put(code,item);
 
         // Add scheme and version back in for redisplay
         request.setAttribute("dictionary", codingScheme);
@@ -331,7 +362,7 @@ public String addToCart() throws Exception {
 	}
 
 }
-        updateCartSizeSessionVariable(request);
+        updateCartSizeSessionVariable(request);
 		return "concept_details";
     }
 
@@ -433,7 +464,7 @@ public String exportCartXML() throws Exception {
 
         SearchCart search = new SearchCart();
         ResolvedConceptReference ref = null;
-        HashMap<String, SchemeVersion> versionList = null;
+        HashMap<String, SchemeVersion> versionList = null;
 
     	if (getCount() < 1) {
         	_messageflag = true;
@@ -499,12 +530,12 @@ public String exportCartXML() throws Exception {
             		_logger.debug("Adding NS: " + sv.namespace);
             	}
             }
-
+
 			// Instantiate DefinitionEntry(Rule Set)
-			DefinitionEntry de = new DefinitionEntry();
-			de.setRuleOrder(1L);
+			DefinitionEntry de = new DefinitionEntry();
+			de.setRuleOrder(1L);
 			de.setOperator(DefinitionOperator.OR);
-
+
 			// Instantiate ValueSetDefinitionReference
 			ValueSetDefinitionReference vsdRef = new ValueSetDefinitionReference();
 			vsdRef.setValueSetDefinitionURI("EXPORT:CART_NODES");
@@ -675,8 +706,8 @@ public String exportCartToCSV() throws Exception {
 
             // Don't allow JSF to forward to cart.jsf
             FacesContext.getCurrentInstance().responseComplete();
-        }
-
+        }
+
 		return null;
     }
 
@@ -692,7 +723,7 @@ public static class Concept {
         private String version = null;
         private String url = null;
         private String displayStatus = "";
-        private String displayCodingSchemeName = "[Not Set]";
+        private String displayCodingSchemeName = "[Not Set]";
         private HtmlSelectBooleanCheckbox checkbox = null;
 
         // Getters & setters
@@ -761,16 +792,16 @@ public void setUrl(String url) {
         public String getKey() {
         	return code + " (" + displayCodingSchemeName + " " + version + ")";
         }
-
+
         public HtmlSelectBooleanCheckbox getCheckbox() {
          	if (checkbox == null) checkbox = new HtmlSelectBooleanCheckbox();
             return checkbox;
         }
 
         public void setCheckbox(HtmlSelectBooleanCheckbox checkbox) {
             this.checkbox = checkbox;
-        }
-
+        }
+
         // *** Private Methods ***
 
         private void setSelected(boolean selected) {
@@ -779,7 +810,7 @@ private void setSelected(boolean selected) {
 
         private boolean getSelected() {
         	return this.checkbox.isSelected();
-        }
+        }
 
         private void initDisplayStatus() {
             if (this.codingScheme == null || this.version == null || this.code == null)

software/ncitbrowser/src/java/gov/nih/nci/evs/browser/bean/DefSourceMapping.java

@@ -1,14 +1,45 @@
-/*L
- * Copyright Northrop Grumman Information Technology.
- *
- * Distributed under the OSI-approved BSD 3-Clause License.
- * See http://ncip.github.com/nci-term-browser/LICENSE.txt for details.
- */
-
 package gov.nih.nci.evs.browser.bean;
 
 /**
- * 
+ * <!-- LICENSE_TEXT_START -->
+ * Copyright 2008,2009 NGIT. This software was developed in conjunction 
+ * with the National Cancer Institute, and so to the extent government 
+ * employees are co-authors, any rights in such works shall be subject 
+ * to Title 17 of the United States Code, section 105.
+ * Redistribution and use in source and binary forms, with or without 
+ * modification, are permitted provided that the following conditions 
+ * are met:
+ *   1. Redistributions of source code must retain the above copyright 
+ *      notice, this list of conditions and the disclaimer of Article 3, 
+ *      below. Redistributions in binary form must reproduce the above 
+ *      copyright notice, this list of conditions and the following 
+ *      disclaimer in the documentation and/or other materials provided 
+ *      with the distribution.
+ *   2. The end-user documentation included with the redistribution, 
+ *      if any, must include the following acknowledgment:
+ *      "This product includes software developed by NGIT and the National 
+ *      Cancer Institute."   If no such end-user documentation is to be
+ *      included, this acknowledgment shall appear in the software itself,
+ *      wherever such third-party acknowledgments normally appear.
+ *   3. The names "The National Cancer Institute", "NCI" and "NGIT" must 
+ *      not be used to endorse or promote products derived from this software.
+ *   4. This license does not authorize the incorporation of this software
+ *      into any third party proprietary programs. This license does not 
+ *      authorize the recipient to use any trademarks owned by either NCI 
+ *      or NGIT 
+ *   5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED 
+ *      WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES 
+ *      OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE 
+ *      DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE,
+ *      NGIT, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT, 
+ *      INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, 
+ *      BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 
+ *      LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 
+ *      CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT 
+ *      LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN 
+ *      ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+ *      POSSIBILITY OF SUCH DAMAGE.
+ * <!-- LICENSE_TEXT_END -->
  */
 
 /**