From bd4e43af1173c6302400109df5c98d3cbdbac16a Mon Sep 17 00:00:00 2001
From: ejc12 <ejc12@43c2fc9b-1942-4403-87b2-35b4218f7473>
Date: Mon, 18 Jul 2011 22:12:27 +0000
Subject: [PATCH] NIHVIVO-2936 Added info about deprecated vivo-basic theme.

---
 doc/upgrade-1.3.html | 32 +++++++++++++++++++++++---------
 1 file changed, 23 insertions(+), 9 deletions(-)

diff --git a/doc/upgrade-1.3.html b/doc/upgrade-1.3.html
index 0afa245f..ceeb43ac 100644
--- a/doc/upgrade-1.3.html
+++ b/doc/upgrade-1.3.html
@@ -143,6 +143,9 @@
                     <li>
                         <a href="#triple_store">Triple Store</a>
                     </li>
+					<li>
+						<a href="#theme">Theme Changes</a>
+					</li>
                     <li>
                         <a href="#upgrade_process">The Upgrade Process</a>
                     </li>
@@ -206,9 +209,9 @@
             <ul>
                 <li>
                     If you are still in RDB mode, it is required that you move your 
-                    triple store to SDB while still at V1.2 (see <a href="ejc12_upgrade-1.3.html#triple_store">Triple Store</a>
-                    info 
-                    below).&nbsp; 
+                    triple store to SDB while still at V1.2 
+					(see <a href="#triple_store">Triple Store</a>
+                    info below).&nbsp; 
                     <br>
                 </li>
                 <li>
@@ -236,7 +239,7 @@
                     below for more information. 
                 </li>
             </ul>
-            <h3 id="triple_store">II.&nbsp; Triple Store</h3>
+            <h3 id="triple_store">II. Triple Store</h3>
             <p>
                 VIVO 1.3 now requires you to use Jena's SPARQL database (SDB) for
                 the triple store technology.&nbsp; Jena's legacy relational database
@@ -288,7 +291,16 @@
             </p>
             <p>
             </p>
-            <h3 id="upgrade_process">III. The Upgrade Process</h3>
+			<h3 id="theme">III. Theme Changes</h3>
+			<p>
+				The vivo-basic theme was deprecated with VIVO V1.2 and is not persent in the 
+				V1.3 release as it does not support V1.2 or V1.3 features.  
+				It is highly recommended that you use the wilma theme or modify the 
+				wilma theme for branding and/or to create a custom look and feel. Please see the 
+				<a href="http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Site_Administrator_Guide">Site Aministration Guide</a> 
+				for more information about customizing your theme.
+			</p>
+            <h3 id="upgrade_process">IV. The Upgrade Process</h3>
             <p>
                 1. Download the new distribution file and unpack it into a new 
                 source directory. 
@@ -756,7 +768,7 @@
             <p>
                 6. Start Apache Tomcat and log in to VIVO. 
             </p>
-            <h3 id="ontology">IV. Ontology Changes</h3>
+            <h3 id="ontology">V. Ontology Changes</h3>
             <h4 id="verify_ontology_upgrade">i. Verify Ontology upgrade process</h4>
             <p>
                 After Apache Tomcat is started, these files should be reviewed to
@@ -866,7 +878,7 @@
                     new default value will be propagated to the knowledge base. 
                 </dd>
             </dl>
-            <h3 id="template">V. Template changes</h3>
+            <h3 id="template">VI. Template changes</h3>
             <ul>
                 <li>
                     <p>
@@ -907,12 +919,14 @@
                     functionality. 
                 </li>
             </ul>
-            <h3 id="listview">VI. List view changes</h3>
+            <h3 id="listview">VII. List view changes</h3>
             <code>&lt;query-base&gt;</code>
             and <code>&lt;query-collated&gt;</code>
             have been replaced with a single query <code>&lt;query-select&gt;</code>
             that contains tags for fragments to be used only in the collated 
-            version of the query. This and other changes are documented in <code>/vitro/doc/list_view_configuration_guidelines.txt</code>.<h3 id="authorization">VII. Authorization changes</h3>
+            version of the query. This and other changes are documented in <code>/vitro/doc/list_view_configuration_guidelines.txt</code>.
+			
+			<h3 id="authorization">VIII. Authorization changes</h3>
             <p>
                 In release 1.3, the VIVO authorization system has some extensive 
                 changes. In summary, these are: