From 9b18989c1d50ee2c281724807caed73ec629a652 Mon Sep 17 00:00:00 2001
From: stellamit <stellamit@43c2fc9b-1942-4403-87b2-35b4218f7473>
Date: Mon, 12 Dec 2011 18:25:10 +0000
Subject: [PATCH] latest upgrade doc from 14 branch

---
 doc/upgrade-1.4.html | 109 +++++++++++++++++++++++--------------------
 1 file changed, 59 insertions(+), 50 deletions(-)

diff --git a/doc/upgrade-1.4.html b/doc/upgrade-1.4.html
index 49309107..43adef64 100644
--- a/doc/upgrade-1.4.html
+++ b/doc/upgrade-1.4.html
@@ -31,15 +31,11 @@
                 or software requirements for V1.4). 
             </p>
             <p>
-              For a description of the release contents see the <a href="TODOaddLinkToAnnouncement">Release announcement for V1.4</a>.
+              For a description of the release contents see the <a href="./release.html">Release announcement for V1.4</a>.
             </p> 
             <hr/>
             <!-- Upgrade process for V1.4 --><h3 id="tableofcontents">Table of Contents</h3>
             <toc>
-                <ol class="roman1">
-                    <li>
-                        <a>Upgrade process for V1.4</a>
-                        <br>
                         <ol class="roman2">
                            <li>
                               <a href="#preparation">Before Performing the Upgrade</a>
@@ -49,18 +45,15 @@
                               <br>
 	                          <ol class="roman2">
 	                             <li>
-	                               <a href="#template_changes">Template changes</a>
+	                               <a href="#newproperty">New Property in deploy.properties</a>
 	                             </li>
 	                             <li>
-	                               <a href="#proxy_editing">Profile editing by Proxies</a>
-	                             </li>
-	                             <li>
-	                               <a href="#tomcat_setup">Change to Tomcat configuration</a>
+	                               <a href="#changetoconfig">Change to tomcat configuration</a>
 	                             </li>
 	                          </ol>
                            </li>
                            <li>
-                             <a href="#upgrade_process">The Upgrade Process</a>
+                             <a href="#upgrade_process">Upgrade Instructions</a>
                            </li>
                            <li>
                               <a href="#kbm">Knowledge Base Migration</a>
@@ -73,7 +66,6 @@
                                 </li>
                               </ol>
                            </li>
-                        </ol>
                     <li>
                         <a href="#termsofuse">Review the VIVO Terms of Use</a>
                     </li>
@@ -85,16 +77,19 @@
             <hr/>
             <h3 id="preparation">I. Before Performing the Upgrade</h3>
             <br/>
-                Create backups of the: 
+                Create backups of: 
             <ul style="list-style-type: square;">
                 <li>
-                    Tomcat webapps directory 
+                    The VIVO distribution directory (which contains the source for VIVO 1.3)
                 </li>
                 <li>
-                    Original source directory  (TODO: I think we should specifically name the directory (I don't know what's intended) sjm) 
+                    The VIVO home directory (pointed to by your deploy.properties file)
                 </li>
                 <li>
-                    MySQL database (mysqldump) 
+                    The webapps directory in Tomcat 
+                </li>
+                <li>
+                    MySQL database (most people use mysqldump to create the backup) 
                 </li>
             </ul>
             <p>
@@ -116,45 +111,45 @@
                 <li>
                     The first time Apache Tomcat starts up after the upgrade, an automated 
                     process will modify the knowledge base to align the  
-                    data with any ontology updates made for the new release. See the section on the <a href="#ontology">Ontology Upgrade</a>
-                    below for more information. Note that 
+                    data with any ontology updates made for the new release. See the section on the <a href="#kbm">Knowledge Base Migration</a>
+                    below for more information. 
                 </li>
             </ul>
 
             <h3 id="changes">II. Noteworthy Changes</h3>
-            
-                <p>(TOTO: I think this should contain only changes to the upgrade process itself. Changes to the source code that are too detailed for the release announcement could go in
-                an appendix (final section) to this document until such time as there is an granual release changes document.</p>
-                
-                <h4 id="template_changes">i. Template changes
-                </h4>
-                <ul>
-	                <li><code>${stylesheets.list}</code>, <code>${scripts.list}</code>, and <code>${headscripts.list}</code> have changed to 
-	                    <code>${stylesheets.list()}</code>, <code>${scripts.list()}</code>, and <code>${headscripts.list()}</code>, respectively.
-	                </li>
-                (ryounes)
-                </ul>
+            	<ul>
+            	    <li>
+                	    <h4 id="newproperty">New property in deploy.properties</h4>
+                	    <p>
+            	            <code>proxy.eligibleTypeList</code> describes which classes of Individuals are 
+             	            eligible for "self-editing" by proxy.
+             	            See the table in <a href="#upgrade_process">Section III</a> for more details.
+             	        </p>
+                	</li>
+            	    <li>
+                	    <h4 id="changetoconfig">Change to Tomcat configuration</h4>
+                        <p>
+                            In order for VIVO to correctly handle international characters,
+                            you must configure Tomcat to conform to the URI standard by
+                            accepting percent-encoded UTF-8.
+                        </p>
+                        <p>
+                            Edit Tomcat's conf/server.xml and add the following attribute to each of the
+                            Connector elements: URIEncoding="UTF-8".
+                        </p>
+                        <pre>
+                    &lt;Server ...&gt;
+                      &lt;Service ...&gt;
+                        &lt;Connector ... URIEncoding="UTF-8"/&gt;
+                          ...
+                        &lt;/Connector&gt;
+                      &lt;/Service&gt;
+                    &lt;/Server&gt;
+                        </pre>
+                	</li>
+               </ul>
 
-                <h4 id="proxy_editing">ii. Profile editing by Proxies
-                </h4>
-                <ul>
-	                <li>addition to deploy.properties</li>
-	                <li> What types of individuals may have proxy editors?
-	                <pre>proxy.eligibleTypeList = http://xmlns.com/foaf/0.1/Person, http://xmlns.com/foaf/0.1/Organization</pre>
-	                </li>
-                (jblake)
-                </ul>
-            
-                <h4 id="tomcat_setup">iii. Change to Tomcat configuration
-                </h4>
-                <ul>
-                    <li>Tomcat configuration</hli>
-                    <li>Specify URI encoding
-                    </li>
-                </ul>
-                (jblake)
-
-            <h3 id="upgrade_process">III. The Upgrade Process</h3>
+            <h3 id="upgrade_process">III. Upgrade Instructions</h3>
                 <p>
                     1. Download the new distribution file and unpack it into a new 
                     source directory. 
@@ -588,6 +583,20 @@
                             /usr/local/vivo/harvester/ 
                         </td>
                     </tr>
+                    <tr>
+                        <td colspan="2">
+                          Types of individual for which we can create proxy editors.
+                          If this is omitted, defaults to http://www.w3.org/2002/07/owl#Thing
+                        </td>
+                    </tr>
+                    <tr class="odd_row blue">
+                        <td>
+                          proxy.eligibleTypeList
+                        </td>
+                        <td>
+                           http://xmlns.com/foaf/0.1/Person, http://xmlns.com/foaf/0.1/Organization
+                        </td>
+                    </tr>
                 </tbody>
             </table>