From b1ef3ae3a94c290dae8bd139cbdf335849c230a2 Mon Sep 17 00:00:00 2001 From: ejc12 Date: Sun, 16 Jan 2011 01:05:11 +0000 Subject: [PATCH] Moving changes I made in the trunk since the branch was created. I'll work out of here forward. --- doc/css/doc.css | 48 +++- doc/html/upgrade-1.2.html | 365 ++++++++++++++++++++++++++ doc/install.html | 213 +++++++-------- doc/install.txt | 530 -------------------------------------- 4 files changed, 508 insertions(+), 648 deletions(-) create mode 100644 doc/html/upgrade-1.2.html delete mode 100644 doc/install.txt diff --git a/doc/css/doc.css b/doc/css/doc.css index 7110bcc3..c1e22f94 100644 --- a/doc/css/doc.css +++ b/doc/css/doc.css @@ -21,7 +21,7 @@ body{ padding: 0; height: 100%; /* needed for container min-height */ font-family: 'Arimo', "Lucida Sans Unicode","Lucida Grande", Geneva, helvetica, sans-serif; - /*font-size: 62.5%;*/ + font-size: 1em; height: auto !important; /* real browsers */ height: 100%; /* IE6: treaded as min-height*/; min-height: 100%; /* real browsers */ @@ -31,10 +31,15 @@ body{ background: #f3f3f0 url(../images/header-background.png) center 0 no-repeat; } /* h1,h2,h3,h4,h5,h6 ------> */ -h2{ - padding: 10px 0 12px 0; +h1 { + padding: 8px 0 6px 0; margin: 0; - font-size: 22px; + font-size: 1.5em; +} +h2 { + padding: 8px 0 6px 0; + margin: 0; + font-size: 1.4em; color: #2485ae; } h2 a{ @@ -47,21 +52,21 @@ h2 a:hover, h2 a:active{ text-decoration: none; } h3{ - padding: 10px 0 12px 0; + padding: 8px 0 6px 0; margin: 0; - font-size: 18px; + font-size: 1.2m; color: #2485ae; } h4{ - padding: 10px 0 12px 0; + padding: 4px 0 4px 0; margin: 0; - font-size: 16px; - color: #2485ae; + font-size: 1.1em; + color: #000000; } h5{ - padding: 10px 0 12px 0; + padding: 3px 0 2px 0; margin: 0; - font-size: 14px; + font-size: 1em; color: #2485ae; } @@ -75,6 +80,16 @@ a:visited { color: #5e6363; } +code, pre { + font-size: 1.1em; +} + +blockquote { + padding: 5px; + font-size: .9em; + background-color: #EEEEEE; +} + /* HEADER ------> */ #branding { position: relative; @@ -110,7 +125,6 @@ h1.vivo-logo a { /* TOC -------> */ ol { - list-style-type: upper-roman; margin: 0 0 10px 10px; } @@ -225,4 +239,12 @@ p{ .displace { position: absolute; left: -9999px; -} \ No newline at end of file +} + +ol.roman1 { + list-style-type: upper-roman; +} + +ol.roman2 { + list-style-type: lower-roman; +} diff --git a/doc/html/upgrade-1.2.html b/doc/html/upgrade-1.2.html new file mode 100644 index 00000000..621e3b1a --- /dev/null +++ b/doc/html/upgrade-1.2.html @@ -0,0 +1,365 @@ + + + + + VIVO + + + + + +
+

VIVO Release 1 v1.2 Upgrade Guide

+ January 28, 2011 - Upgrading from Release 1 v1.1 to Release 1 v1.2 +
+ Missing pieces and fixes +
    +
  • + Link to install pdf online at SF +
    • +
  • +
    • +
  • +
    • +
+
+ + + +

+ This document provides a short description of the steps involved in upgrading your + installation of VIVO from Release 1, Version 1.1 to Version 1.2. This and other + documentation can be found on the support page + at VIVOweb.org +

+

+ If you need to do a fresh install, please consult + VIVO Release 1 v1.2 Installation Guide + or the install.html file located in the + + doc + + directoy of the VIVO source code distribution. +

+

Release anouncement for V1.2

+

+ Text from the wiki page +

+

Upgrade process for V1.2

+

+ +
    +
  1. + Before Performing the Upgrade +
    2. +
  2. + The Upgrade Process +
    3. +
  3. + Ontology Upgrade +
    4. +
      +
    1. + Verify Ontology upgrade process +
      2. +
    2. + Ontology knowledge base manual review +
      3. +
    +
  4. + Theme Modifications +
    5. +
+ +

I. Before Performing the Upgrade

+

+ Please ensure that backups are created of the: +

+ +

+ The upgrade process is similar to the original install process with the following + EXCEPTIONS: +

+ +

The Upgrade Process

+
    +
  1. + Download the new distribution file and unpack it into a new source + directory. +
    2. +
  2. + Create deploy.properties, using the same values as in your previous + installation and set values for the new variables. +
    3. +
  3. + Apply any previous changes you have made to the new source directory. +
    + Special notes regarding source files +
      +
    • + This process assumes any changes made to the application were made in + the source directory and deployed, and were not made directly within + the Tomcat webapps directory. +
      • +
    • In many cases, simply copying the modified files from your original + source directory will not work since the files on which they are based + have changed. It will be necessary to inspect the new source files and + add any changes to them at that time.
      • +
    • + NIH-funded VIVO Implmentations will need to apply the Google Analytics Tracking + Code (GATC) to + + googleAnalytics.ftl + + in the theme:
      [new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl
      + A sample + + googleAnalytics.ftl + + is included in the built-in theme. This file + serves only as an example, and you must replace the tracking code shown + with your institution's own tracking code. + For additional information about the GATC for the NIH-funded VIVO + implementation sites and a copy your institution's tracking code, see the + VIVO Google Analytics wiki page. +
      • +
    • + If you had used the vivo/contrib/FLShibboleth code in your previous release, + you should stop using it. Consult install.html or VIVO Release 1 v1.2 Installation Guide + on "Using an External Authentication System with VIVO". +
      • +
    +
    +
    4. +
  4. + If you had modified + + web.xml + + to configure the Pellet Reasoner (as described + in the installation instructions), repeat that modification. +
    5. +
  5. + Stop Apache Tomcat and run ant by typing: + + ant all + +
    6. +
  6. + Start Apache Tomcat and log in to VIVO. +
    7. +
+ 
+
+
+-------------------------------------------------------------------------------
+
+III. Ontology Changes
+
+A. Verify Ontology upgrade process
+
+After Apache Tomcat is started, these files should be reviewed to verify that
+the automated upgrade process was executed successfully.  The ontology alignment 
+process will create the following files in the Tomcat webapps/vivo/WEB-INF directory:
+
+ontologies/update/logs/knowledgeBaseUpdate.log 
+    A log of a summary of updates that were made to the knowledge base and notes 
+    about some recommended manual reviews. This file should end with
+    "Successfully finished processing ontology changes".
+    
+ontologies/update/logs/knowledgeBaseUpdate.error.log 
+    A log of errors that were encountered during the upgrade process. This file
+    should be empty if the upgrade was successful.
+    
+ontologies/update/changedData/removedData.n3
+    An N3 file containing all the statements that were removed from the knowledge base.
+    
+ontologies/update/changedData/addedData.n3
+    An N3 file containing all the statements that were added to the knowledge base.
+
+B. Ontology knowledge base manual review
+
+Changes to the VIVO core ontology may require corresponding
+modifications of the knowledge base instance data and local ontology
+extensions.
+
+When Apache Tomcat starts up following the upgrade, it will initiate 
+a process to examine the knowledge base and apply necessary changes.
+Not all of the modifications that may be required can be automated,
+so manual review of the knowledge base is recommended after the
+automated upgrade process. The automated process will make only 
+the following types of changes:
+
+  Class or Property renaming
+    All references to the class (in the subject or object position) will
+    be updated to the new name. References to the property will be
+    updated to the new name.
+  
+  Class or Property deletion
+    All individuals in a deleted class will be removed.
+   
+    All statements using a deleted property will be changed
+    to use the nearest available superproperty. If there is no available
+    superproperty then the statement will be deleted from the
+    knowledge base. Note that all removed and added data
+    is recorded in the files in the changedData directory.
+    
+  Property addition
+    If a newly added property is the inverse of a previously
+    existing property, the inverse of any statements using the
+    pre-existing property will be asserted.
+
+  Annotation property default values
+    If a site has modified the value of a vitro annotation (such as
+    displayRankAnnot or displayLimitAnnot) so that it is
+    no longer using the default, then that setting will be left unchanged.
+    If a site is using the default value of a vitro annotation, and the
+    default has been changed in the new version of the ontology, then
+    the new default value will be propagated to the knowledge base.
+
+-------------------------------------------------------------------------------
+
+IV. Theme Changes
+
+VIVO 1.1 introduces the first step in a transition from JavaServer Pages (JSPs)
+to the FreeMarker template engine for generating web pages. As part of this 
+process, the JSP files that were used for theme customization in earlier 
+versions of VIVO have been replaced by a set of FreeMarker templates. 
+In the 1.1 install package, these files are located in 
+/vivo/themes/vivo-basic/templates and have an ftl (for FreeMarker Template
+Language) extension.
+
+Follow step A or B below, whichever is applicable to your site:
+
+A. If you did not create a customized theme for your site in VIVO 1.0, but used
+the 1.0 vivo-basic theme in its original directory, you need not take any 
+action in order to convert your site to the VIVO 1.1 theme.
+
+B. If you created your own theme directory in VIVO 1.0, follow the steps below
+under sections "Templates," "Stylesheets,"  and "Site Icons" to upgrade your 
+theme to VIVO 1.1.
+
+    1. Templates
+
+       a. Copy the directory /vivo/themes/vivo-basic/templates into your theme
+          directory /vivo/themes/.
+
+       b. Follow step i or ii below, whichever is applicable to your theme. 
+
+           i. If you did not apply any customizations to the JSPs in your VIVO  
+              1.0 theme, then you do not need to apply any additional changes 
+              to the VIVO 1.1 theme templates during the upgrade process.
+
+           ii. If you did apply customizations to the JSPs in your VIVO 1.0  
+               theme,you will need to hand-replicate those modifications in the 
+               new theme template files. 
+           
+               The theme template content that was previously contained in 
+               three JSP files is now contained in five FTL files. The 
+               correspondence between the 1.0 JSPs and the 1.1 FTLs is as 
+               follows:
+               
+                   identity.jsp => identity.ftl
+                   menu.jsp => menu.ftl and search.ftl
+                   footer.jsp => footer.ftl and googleAnalytics.ftl
+    
+               googleAnalytics.ftl is a new file to which you will add
+               your site's Google Analytics Tracking Code (see section II).
+           
+               Because the FreeMarker Template Language uses many syntactic 
+               conventions that will be familiar to template authors from JSP 
+               or other common templating systems, the translation of your JSP 
+               changes into the new FTLs should be relatively straightforward. 
+   
+               Consult the FreeMarker Template Author's Guide at 
+               http://freemarker.org/docs/dgui.html and the Reference at 
+               http://freemarker.org/docs/ref.html for complete documentation  
+               of the syntax and available built-in constructs. Template 
+               authors need  not be concerned with the Programmer's Guide or 
+               Java API documentation.
+
+       c. Remove the jsp directory from your themes directory.
+    
+    2. Stylesheets
+        
+       VIVO 1.1 includes changes to vivo-basic stylesheets. If you modified 
+       styles in your VIVO 1.0 theme, you will not be able to simply copy the  
+       1.0 stylesheets into your 1.1 theme, because you will then lose 1.1 
+       style upgrades that your theme should pick up.  Instead, you should 
+       use the vivo-basic 1.1 stylesheets as a starting point, and manually
+       merge your 1.0 style modifications in as needed.
+    
+    3. Site Icons
+    
+       Copy the site icons from your 1.0 theme into the site_icons folder in
+       your 1.1 theme.		
+		
+		
+		
+		
+		
+
+
+ + + + diff --git a/doc/install.html b/doc/install.html index a02cabe5..b3df7c0f 100644 --- a/doc/install.html +++ b/doc/install.html @@ -12,17 +12,17 @@

VIVO Release 1 V1.2 Installation Guide

+ + January 28, 2011 +
Missing pieces and fixes
  • - SDB - any checks? (BL/SM) + Add release announcemnet
  • - Theme changes, file locations, branding issues (NC/MB) -
    • -
  • - Fix styles on file, dir, parameters name styles + Link to upgrade pdf online at SF
@@ -43,7 +43,7 @@

Installation process for V1.2

This document is a summary of the VIVO installation process. This and other - documentation can be found on the spport page + documentation can be found on the support page at VIVOweb.org

- Be sure to setup the environment variables for "JAVA_HOME" and "ANT_HOME" + Be sure to setup the environment variables for + and ANT_HOME and add the executables to your path per your operating system and installation directions from the software support web sites.

II. Create an empty MySQL database

- Decide on a database name, username, and password. Log into your - MySQL server and create a new database in MySQL that uses UTF-8 - encoding. You will need  these values for step IV when you - configure the deployment properties. At the MySQL command line you can - create the database and user with these commands  substituting - your values for "dbname", "username", and "password". Most of the time, - the "hostname" will equal "localhost". + Decide on a database name, username, and password. Log into your + MySQL server and create a new database in MySQL that uses UTF-8 + encoding. You will need these values for Step IV when you + configure the deployment properties. At the MySQL command line you can + create the database and user with these commands substituting + your values for dbname, username, and password. Most of the time, + the hostname will equal localhost. 

                 CREATE DATABASE dbname CHARACTER SET utf8;
@@ -158,29 +159,29 @@
                 

             
             

-                Download the VIVO application source as either rel-1.1.1.zip or
-                rel-1.1.1.gz file and unpack it on your web
-                server:
+                Download the VIVO application source as either rel-1.2.zip
+                or rel-1.2.gz
+                file and unpack it on your web server:
                 

                 http://vivoweb.org/download
             

             
IV. Specify deployment properties 

             

-                At the top level of the unpacked distribution, copy the file
-                "example.deploy.properties" to a file named simply "deploy.properties".
+                At the top level of the unpacked distribution, copy the file example.deploy.properties
+                to a file named simply deploy.properties.
                 This file sets several properties used in compilation and deployment.
             

             

                 Windows:
-                For those installing on Windows operating system, include the
-                windows drive and use the forward slash "/" and not the back slash "\"
-                in the directory locations, e.g. "c:/tomcat".
+                For those installing on Windows operating system, include the 
+                windows drive and use the forward slash "/" and not the back slash "\" 
+                in the directory locations, e.g. c:/tomcat.
             

             

                 External authentication:
                 If you want to use an external authentication system like Shibboleth or 
-                CUWebAuth, you will need to set two additional properties in this file. 
-                See the section below entitled "Using an External Authentication System with VIVO".
+                CUWebAuth, you will need to set two additional properties in this file.  
+                See the section below entitled Using an External Authentication System with VIVO.
             

             
@@ -196,14 +197,12 @@
                         Default namespace: VIVO installations make their RDF resources available 
                         for harvest using linked data. Requests for RDF resource URIs redirect to HTML  
                         or RDF representations as specified by the client. To make this possible, 
-                        VIVO's default namespace must have certain structure and  begin with the public  
+                        VIVO's default namespace must have certain structure and begin with the public  
                         web address of the VIVO installation. For example, if the web address of a VIVO 
                         installation is "http://vivo.example.edu/" the default namespace must be set to  
                         "http://vivo.example.edu/individual/" in order to support linked data. Similarly, 
                         if VIVO is installed at "http://www.example.edu/vivo" the default namespace must be  
-                        set to "http://www.example.edu/vivo/individual/" 
-                        

-                        * The namespace must end with "individual/" (including the trailing slash).
+                        set to "http://www.example.edu/vivo/individual/" 
* The namespace must end with "individual/" (including the trailing slash).

@@ -385,9 +384,9 @@
                 
@@ -402,8 +401,8 @@
                 
@@ -498,8 +497,7 @@
                 in order to serve Web requests quickly (the in-memory copy and the  
                 underlying databaseare kept in synch as edits are performed). 
                 

-                    VIVO will 
-                    require more memory than that allocated to Tomcat by default. With most  
+                    VIVO will require more memory than that allocated to Tomcat by default. With most 
                     installations of Tomcat, the "setenv.sh" or "setenv.bat" file in Tomcat's 
                     bin directory is a convenient place to set the memory parameters.
                     

@@ -517,16 +515,14 @@
                     data, 256m to 512m should be sufficient.
                 

-                    If an OutOfMemoryError is 
-                    encountered during VIVO execution, it can be remedied by increasing the  
-                    heap parameters and restarting Tomcat. 
+                    If an OutOfMemoryError is encountered during VIVO execution, it can 
+                    be remedied by increasing the heap parameters and restarting Tomcat. 
                 

-                    Security limits: VIVO is a 
-                    multithreaded web application that may require more threads than are  
-                    permitted under your Linux installation's default configuration. Ensure 
-                    that your installation can support the required number of threads 
-                    by making the following edits to "/etc/security/limits.conf":
+                    Security limits: VIVO is a multithreaded web application that may 
+                    require more threads than are permitted under your Linux installation's  
+                    default configuration. Ensure that your installation can support the 
+                    required number of threads by making the following edits to /etc/security/limits.conf:
                 
                     apache	hard	nproc	400
@@ -534,18 +530,19 @@
                 
VII. Start Tomcat 

-                    Most Tomcat installations can be started by running "startup.sh" or 
-                    "startup.bat" in Tomcat's bin directory. Point your browser to  
-                    "http://localhost:8080/vivo/" to test the application. If Tomcat does not 
-                    start up, or the VIVO application is not visible, check the  
-                    catalina.out file in Tomcat's logs directory. 
+                    Most Tomcat installations can be started by running startup.sh
+                    or startup.bat
+                    in Tomcat's bin directory. Point your browser to 
+                    "http://localhost:8080/vivo/" to test the application. If Tomcat does not  
+                    start up, or the VIVO application is not visible, check the catalina.out
+                    file in Tomcat's logs directory. 
                 
VIII. Log in and add RDF data 

                     If the startup was successful, you will see a welcome message 
                     informing you that you have successfully installed VIVO. Click the "Log in" link  
-                    near the upper right corner.  Log in with the initialAdminUser
-                    username you set up in Step IV. The initial password for the initialAdminUser
+                    near the upper right corner.  Log in with the initialAdminUser
+                    username you set up in Step IV. The initial password for the initialAdminUser
                     account is "defaultAdmin" (without the quotes). On first login, you will be
                     prompted to select a new password and verify it a second time.
                 

@@ -580,7 +577,7 @@
             
IX. Set the Contact Email Address (if using "Contact Us" form)

                 If you have configured your application to use the "Contact Us"
-                feature in Step IV (Vitro.smtpHost), you will also need to add an email address
+                feature in Step IV (Vitro.smtpHost), you will also need to add an email address
                 to the VIVO application.  This is the email that the contact form
                 submits to. It can be a list server or an individual's
                 email address.
@@ -588,12 +585,12 @@
             

                 Log in as a system administrator. Navigate to the
                 "Site Admin" table of contents (link in the right side of the header).
-                Go to "Site Information" (under "Site Configuration").  In the
+                Go to "Site Information" (under "Site Configuration"). In the
                 "Site Information Editing Form," enter a functional email address in
                 the field "Contact Email Address." and submit the change.
             

-                If you set theVitro.smtpHost
+                If you set theVitro.smtpHost
                 in Step IV and do NOT provide an email addressin this
                 step, your users will receive a java error in the interface.
             

@@ -610,14 +607,13 @@
             

                 Using the mod_jk connector allows for communication between Tomcat 
-                and the primary web server. The Quick
-                    Start HowTo
+                and the primary web server. The Quick Start HowTo
                 on the Apache site describes the minimum server configurations 
                 for several popular web servers. 
             

-                After setting up the mod_jk connector above, you will need to
-                modify the Tomcat's server.xml ([tomcat root]/conf/) to respond to
+                After setting up the mod_jk connector above, you will need to 
+                modify the Tomcat's server.xml (located in [tomcat root]/conf/) to respond to
                 requests from Apache via the connector. Look for the
                 <connector> directive and add the following properties:
             

@@ -626,13 +622,15 @@
             

                 Note: the value for maxThreads (320) is equal to the value for MaxClients 
-                in the apache's "httpd.conf" file. 
+                in the apache's httpd.conf
+                file. 
             

-                Locate the <Host name="localhost"...> directive and update as
+                Locate the <Host name="localhost"...>
+                directive and update as
                 follows:
             

-            
+            
 	    <Host name="localhost" appBase="webapps"
 	        DeployOnStartup="false"
 	        unpackWARs="true" autoDeploy="false"
@@ -666,9 +664,9 @@
             

                 By default, Pellet is fed only an incomplete view of 
                 your ontology and only certain inferences are materialized. These  
-                include rdf:type,  rdfs:subClassOf,owl:equivalentClass, and 
+                include rdf:type, rdfs:subClassOf, owl:equivalentClass, and 
                 owl:disjointWith. This mode is typically suitable for ontologies with a  
-                lot of instance data.  If you would like to keep the default mode, 
+                lot of instance data. If you would like to keep the default mode, 
                 skip to the next step. 
             

             

@@ -679,19 +677,17 @@
             

                 Then change the name of the listener class to 
                 PelletReasonerSetupComplete. Because "complete" reasoning can be very  
-                resource intensive, there is also an  option to materialize nearly 
+                resource intensive, there is also an option to materialize nearly 
                 all inferences except owl:sameAs and owl:differentFrom. 
             

             

-                This is enabled 
-                by specifying PelletReasonerSetupPseudocomplete. For ontologies with  
-                large numbers of individuals, this mode can offer enormous performance 
+                This is enabled by specifying PelletReasonerSetupPseudocomplete. For ontologies 
+                with large numbers of individuals, this mode can offer enormous performance  
                 improvements over the "complete" mode. 
             

             

-                Finally, a class called
-                PelletReasonerSetupPseudocompleteIgnoreDataproperties is provided to
-                improve performance on ontologies with large literals where data
+                Finally, a class called PelletReasonerSetupPseudocompleteIgnoreDataproperties 
+                is provided to improve performance on ontologies with large literals where data
                 property entailments are not needed.
             

             

@@ -721,10 +717,7 @@
                     external authentication system.
                 

                 

-                    For VIVO, this secured page is named: 
-                    
-                        /loginExternalAuthReturn
-                    
+                    For VIVO, this secured page is named: /loginExternalAuthReturn
                 

                 

                     When your instructions call for the location of the secured page, this is the 
@@ -732,40 +725,49 @@
                 

                 
Configuring VIVO

                 

-                    To enable external authentication, VIVO requires three values in the 
-                    deploy.properties file.
+                    To enable external authentication, VIVO requires three values in the deploy.properties
+                    file.
                 

                 
    
                     
  • 
-                        The name of the HTTP header that will hold the external user’s network ID 
-                        When a user completes the authentication process, the Apache server will  
-                        put the user’s network ID into one of the headers of the HTTP request. 
-                        The instructions from your institution should tell you which header is  
+                        
    The name of the HTTP header that will hold the external user's network ID.
    
+                        When a user completes the authentication process, the Apache server will 
+                        put the user's network ID into one of the headers of the HTTP request.  
+                        The instructions from your institution should tell you which header is 
                         used for this purpose. 
-                        You need to tell VIVO the name of that HTTP header. Insert a line like  
-                        this in the deploy.properties file: 
    externalAuth.netIdHeaderName = [the header name]
    
-                        For example: 
    externalAuth.netIdHeaderName = remote_userID
    
+                        
    
+                            You need to tell VIVO the name of that HTTP header. Insert a line like 
+                            this in the deploy.properties file: 
    externalAuth.netIdHeaderName = [the header name]
    
+                            For example: 
+                        
    
+                        
    externalAuth.netIdHeaderName = remote_userID
    
                     
    • 
                     
  • 
-                        The text for the Login button 
-                        To start the authentication process, the user will click on a button in  
-                        the VIVO login form. You need to tell VIVO what text should appear in that 
-                        button.  
-                        Put a line like this in the deploy.properties file: 
-                        externalAuth.buttonText = [the text for your login button]  
-                        For example: 
    externalAuth.buttonText = Log in using BearCat Shibboleth
    
-                        The VIVO login form will display a button labelled “Log in using BearCat 
-                        Shibboleth”.
+                        
    The text for the Login button.
    
+                        To start the authentication process, the user will click on a button in 
+                        the VIVO login form. You need to tell VIVO what text should appear in that  
+                        button. 
+                        
    
+                            Put a line like this in the deploy.properties file: 
+                            externalAuth.buttonText = [the text for your login button]  
+                            For example: 
+                        
    
+                        
    externalAuth.buttonText = Log in using BearCat Shibboleth
    
+                        The VIVO login form will display a button labelled "Log in using BearCat 
+                        Shibboleth".
                     
    • 
                     
  • 
-                        Associating a User with a profile page 
-                        If VIVO has an account for the user, the user will be given the privileges  
+                        
    Associating a User with a profile page
    
+                        If VIVO has an account for the user, the user will be given the privileges 
                         assigned to that account. 
-                        In addition, VIVO will try to associate the user with a profile page, so  
-                        the user may edit his own profile data. VIVO will search the data model 
-                        for a person with a property that matches the User’s network ID.  
-                        You need to tell VIVO what property should be used for matching. Insert 
-                        a line like this in the deploy.properties file:
    selfEditing.idMatchingProperty = [the URI of the property]
    
+                        
    
+                            In addition, VIVO will try to associate the user with a profile page, so 
+                            the user may edit his own profile data. VIVO will search the data model  
+                            for a person with a property that matches the User’s network ID. 
+                            You need to tell VIVO what property should be used for matching. Insert 
+                            a line like this in the deploy.properties file:
+                        
    
+                        
    selfEditing.idMatchingProperty = [the URI of the property]
    
                         For example:
    selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId
    
                     
    • 
                 

@@ -808,7 +810,8 @@
             
    
                 
  • 
                     Point your browser to the home page of your website, and click the "Log in" link 
-                    near the upper right corner. Log in with the initialAdminUser username you  
+                    near the upper right corner. Log in with the initialAdminUser
+                    username you 
                     set up in Step IV. If this is your first time logging in, you will be 
                     prompted to change the password.
                 
    • 
@@ -824,7 +827,7 @@
                     the next step. 
                 
                 
  • 
-                    Open a new web browser or browser tab to the page http://marbles.sourceforge.net/.
+                    Open a new web browser or browser tab to the page http://marbles.sourceforge.net/.
                     In the pink box on that page enter the URI of the individual you created in the
                     previous step and click "open."
                 
    • 
@@ -841,11 +844,11 @@
             
    
             
      
                 
    • 
-                    The search box is on the right side, directly opposite the "Index" link. 
-                    Type the word "Australia" into the box, and click on the "Search"  
+                    Type the word "Australia" into the search box, and click on the Search 
                     button.You should see a page of results, with links to countries that 
-                    border Australia, individuals that include Australia, and to 
-                    Australia itself.
+                    border Australia, individuals that include Australia, and to  
+                    Australia itself.  To trigger the search index, you can log in as a site 
+                    administrator and go to "http://your-vivo-url/SearchIndex".
                 
      • 
             
    
         
diff --git a/doc/install.txt b/doc/install.txt
deleted file mode 100644
index 2deeb1c3..00000000
--- a/doc/install.txt
+++ /dev/null
@@ -1,530 +0,0 @@
-
--------------------------------------------------------------------------------
- 
-This document is a summary of the VIVO installation process. This and other documentation
-can be found at:
-
-     http://vivoweb.org/support
-    
-PLEASE NOTE!
-These instructions assume that you are performing a clean install, 
-including emptying an existing database and removing a previous installation 
-from the Tomcat webapps directory. Product functionality may not be as expected 
-if you install over an existing installation of an earlier version.
-
-Upgrade:
-If you are going to upgrade an existing service, please consult the upgrade.txt
-in this directory.
-
-VIVO Developers:
-If you are working on the VIVO source code from Subversion, the instructions 
-are slightly different. Please consult developers.txt in this directory.
- 
--------------------------------------------------------------------------------
- 
-    * I. Install required software
-    * II. Create an empty MySQL database
-    * III. Download the VIVO Application Source
-    * IV. Specify deployment properties
-    * V. Compile and deploy
-    * VI. Set Tomcat JVM parameters and security limits
-    * VII. Start Tomcat
-    * VIII. Log in and add RDF data
-    * IX. Set the Contact Email Address (if using "Contact Us" form)
-    * X. Setup Apache Tomcat Connector
-    * XI. Configure Pellet Reasoner
-    * XII. Using an External Authentication System with VIVO
-    * XIII. Was the installation successful?
-
--------------------------------------------------------------------------------
- 
-I. Install required software
-
-Before installing VIVO, make sure that the following software is installed on 
-the desired machine:
-
-    * Java (SE) 1.6 or higher [http://java.sun.com] (Not OpenJDK)
-    * Apache Tomcat 6.x or higher [http://tomcat.apache.org]
-    * Apache Ant 1.7 or higher [http://ant.apache.org]
-    * MySQL 5.1 or higher [http://www.mysql.com]
-
-Be sure to setup the environment variables for "JAVA_HOME" and "ANT_HOME" and 
-add the executables to your path per your operating system and installation 
-directions from the software support web sites.
-
--------------------------------------------------------------------------------
- 
-II. Create an empty MySQL database
-
-Decide on a database name, username, and password. Log into your MySQL server 
-and create a new database in MySQL that uses UTF-8 encoding. You will need 
-these values for step IV when you configure the deployment properties. At the 
-MySQL command line you can create the database and user with these commands 
-substituting your values for "dbname", "username", and "password". Most of the 
-time, the "hostname" will equal "localhost".
-
-CREATE DATABASE dbname CHARACTER SET utf8;
-
-Grant access to a database user. For example:
-
-GRANT ALL ON dbname.* TO 'username'@'hostname' IDENTIFIED BY 'password';
-
-Keep track of the database name, username, and password for Step IV.
-
--------------------------------------------------------------------------------
- 
-III. Download the VIVO Application Source
-
-Download the VIVO application source as either rel-1.1.1.zip or rel-1.1.1.gz file 
-and unpack it on your web server:
-      
-      http://vivoweb.org/download
-
--------------------------------------------------------------------------------
- 
-IV. Specify deployment properties
-
-At the top level of the unpacked distribution, copy the file 
-example.deploy.properties to a file named simply deploy.properties. This file 
-sets several properties used in compilation and deployment.
-
-NOTE: For those installing on Windows operating system, include the windows 
-drive and use the forward slash "/" and not the back slash "\" in the 
-directory locations, e.g. "c:/tomcat".
-
-                Default namespace: VIVO installations make their RDF resources available for harvest 
-                using linked data. Requests for RDF resource URIs redirect to HTML 
-                or RDF representations as specified by the client. To make this 
-                possible, VIVO's default namespace must have certain structure and 
-                begin with the public web address of the VIVO installation. 
-                For example, if the web address of a VIVO installation is 
-                http://vivo.example.edu/ the default namespace must be set to 
-                http://vivo.example.edu/individual/ in order to support linked data.
-                Similarly, if VIVO is installed at http://www.example.edu/vivo the 
-                default namespace must be set to http://www.example.edu/vivo/individual/
-                Note:  The namespace must end with "individual/" (including the 
-                trailing slash).
-property name:  Vitro.defaultNamespace 	
-example value:  http://vivo.mydomain.edu/individual/
-
-                Directory where Vitro code is located. In most deployments, 
-                this is set to ./vitro-core, but it commonly points elsewhere 
-                during development.
-property name:  vitro.core.dir
-example value:  ./vitro-core
-
-                Directory where tomcat is installed
-property name:  tomcat.home
-example value:  /usr/local/tomcat
-
-                Name of your VIVO application
-property name:  webapp.name
-example value:  vivo
-
-                Directory where uploaded files will be stored. You must create 
-                this directory ahead of time.
-property name:  upload.directory
-example value:  /usr/local/vivo/data/uploads
-
-                Directory where the Lucene search index will be built. 	
-                Depending on your permissions and who Tomcat is running as, 
-                you may need to create this directory ahead of time.
-property name:  LuceneSetup.indexDir 	
-example value:  /usr/local/vivo/data/luceneIndex
-
-                Specify an SMTP host that the form will use for sending 
-                e-mail (Optional). If this is left blank, the contact form 
-                will be hidden and disabled.
-property name:  Vitro.smtpHost 	
-example value:  smtp.servername.edu
-
-                Specify the JDBC URL of your database.  Change the end of the
-                URL to reflect your database name (if it is not "vivo").
-property name:  VitroConnection.DataSource.url 	
-example value:  jdbc:mysql://localhost/vivo
-
-                Change the username to match the authorized user you created in MySQL
-property name:  VitroConnection.DataSource.username
-example value:  username
-
-                Change the password to match the password you created in MySQL 	
-property name:  VitroConnection.DataSource.password
-example value:  password
-	  
-                Specify the Jena triple store technology to use.  SDB is Jena's
-                SPARQL database; this setting allows RDF data to scale beyond the
-                limits of the JVM heap.  Set to RDB to use the older Jena RDB
-                store with in-memory caching.
-property name:  VitroConnection.DataSource.tripleStoreType
-example value:  SDB
-
-                Specify the maximum number of active connections in the database
-                connection pool to support the anticipated number of concurrent
-                page requests.  It is not necessary to adjust this value when
-                using the RDB configuration.
-property name:  VitroConnection.DataSource.pool.maxActive
-example value:  40
-
-                Specify the maximum number of database connections that will be
-                allowed to remain idle in the connection pool.  Default is
-                25% of the maximum number of active connections.
-property name:  VitroConnection.DataSource.pool.maxIdle
-example value:  10
-	
-                Change the dbtype setting to use a database other than MySQL.
-                Otherwise, leave this value unchanged. 
-                Possible values are DB2, derby, HSQLDB, H2, MySQL, Oracle, 
-                PostgreSQL, and SQLServer.  
-                Refer to http://openjena.org/wiki/SDB/Databases_Supported 
-                for additional information.
-property name:  VitroConnection.DataSource.dbtype
-example value:  MySQL
-                
-                Specify a driver class name to use a database other than MySQL.
-                Otherwise, leave this value unchanged.
-                This JAR file for this driver must be added to the the 
-                webapp/lib directory within the vitro.core.dir specified above.
-property name:  VitroConnection.DataSource.driver
-example value:  com.mysql.jdbc.Driver
-
-                Change the validation query used to test database connections
-                only if necessary to use a database other than MySQL.
-                Otherwise, leave this value unchanged.
-property name:  VitroConnection.DataSource.validationQuery
-example value:  SELECT 1
-
-                Specify the name of your first admin user for the VIVO application. 
-                This user will have an initial temporary password of 'defaultAdmin'. 
-                You will be prompted to create a new password on first login.
-property name:  initialAdminUser 	
-example value:  defaultAdmin
-
-                The name of a property that can be used to associate an Individual
-                with a user account. When a user logs in with a name that matches
-                the value of this property, the user will be authorized to edit
-                that Individual.
-property name:  selfEditing.idMatchingProperty 	
-example value:  http://vivo.mydomain.edu/ns#networkId
-
-NOTE: If you want to use an external authentication system like Shibboleth or
-CUWebAuth, you will need to set two additional properties in this file. See 
-the section below entitled "Using an External Authentication System with VIVO".
-
-                Temporal Graph Visualization is used to compare different 
-                organizations/people within an organization on different parameters 
-                like number of publications, grants. This parameter will be used 
-                as a default in case a URI is not provided. It will be also used 
-                whenever this visualization is to be rendered for top level organization.
-                In absence of this parameter a SPARQL query will be fired which will 
-                attempt to provide a top level organization.The name of a property 
-                that can be used to associate an Individual with a user account. 
-                When a user logs in with a name that matches the value of this property,
-                the user will be authorized to edit that Individual.
-property name:  visualization.topLevelOrg
-example value:  http://vivo-trunk.indiana.edu/individual/topLevelOrgURI
-
-NOTE: If you want to use an external authentication system like Shibboleth or
-CUWebAuth, you will need to set two additional properties in this file. See 
-the section below entitled "Using an External Authentication System with VIVO".
-
--------------------------------------------------------------------------------
- 
-V. Compile and deploy
-
-At the command line, from the top level of the unpacked distribution directory,
-type:
-
-ant all
-
-to build VIVO and deploy to Tomcat's webapps directory.
-
--------------------------------------------------------------------------------
-
-VI. Set Tomcat JVM parameters and security limits
-
-Currently, VIVO copies the contents of your RDF database into memory in order
-to serve Web requests quickly (the in-memory copy and the underlying database
- are kept in synch as edits are performed).
-
-VIVO will require more memory than that allocated to Tomcat by default. With
-most installations of Tomcat, the setenv.sh or setenv.bat file in Tomcat's bin
-directory is a convenient place to set the memory parameters. 
-
-For example: 
-
-export CATALINA_OPTS="-Xms1024m -Xmx1024m -XX:MaxPermSize=64m"
-
-This sets Tomcat to allocate an initial heap of 1024 megabytes, a maximum heap 
-of 1024 megabytes, and a PermGen space of 64 megs. 1024 megabytes is a minimum 
-practical heap size for production installations storing data for large academic 
-institutions, and additional heap space is preferable. For testing with small 
-sets of data, 256m to 512m should be sufficient.
-
-If an OutOfMemoryError is encountered during VIVO execution, it can be remedied 
-by increasing the heap parameters and restarting Tomcat.
-
-Security limits: VIVO is a multithreaded web application that may require more threads than are 
-permitted under your Linux installation's default configuration. Ensure that 
-your installation can support the required number of threads by making the 
-following edits to /etc/security/limits.conf:
-
-    apache    hard    nproc   400
-    tomcat6   hard    nproc   1500 
-
--------------------------------------------------------------------------------
- 
-VII. Start Tomcat
-
-Most Tomcat installations can be started by running startup.sh or startup.bat 
-in Tomcat's bin directory. Point your browser to http://localhost:8080/vivo/ 
-to test the application.
-
-If Tomcat does not start up, or the VIVO application is not visible, check the 
-catalina.out file in Tomcat's logs directory. 
-
--------------------------------------------------------------------------------
- 
-VIII. Log in and add RDF data
-
-If the startup was successful, you will see a welcome message informing you 
-that you have successfully installed VIVO. Click the "Log in" link near the 
-upper right corner. Log in with the initialAdminUser username you set up in 
-Step IV. The initial password for initialAdminUser is defaultAdmin. On first 
-login, you will be prompted to select a new password and verify it a second 
-time.
-
-After verifying your new password, you will be presented with a menu of 
-editing options. Here you can create OWL classes, object properties, data 
-properties, and configure the display of data. Currently, any classes you wish 
-to make visible on your website must be part of a class group, and there a 
-number of visibility and display options available for each ontology entity. 
-
-VIVO comes with a core VIVO ontology, but you may also upload other ontologies 
-from an RDF file. Under the "Advanced Data Tools" click "Add/Remove RDF Data." 
-Note that Vitro currently works best with OWL-DL ontologies and has only limited 
-support for pure RDF data. You can enter a URL pointing to the RDF data you 
-wish to load or upload a file on your local machine. Ensure that the "add RDF" 
-radio button is selected. You will also likely want to check "create 
-classgroups automatically." Clicking the "Index" tab in the navigation bar at 
-the top left of the page will show a simple index of the knowledge base.  
-See more documentation for configuring VIVO, ingesting data, and manually 
-adding data  at http://vivoweb.org/support.
-
--------------------------------------------------------------------------------
-
-IX. Set the Contact Email Address (if using "Contact Us" form)
-
-If you have configured your application to use the "Contact Us" feature in Step
-IV (Vitro.smtpHost), you will also need to add an email address to the VIVO 
-application.  This is the email that the contact form submits to.  It can be a 
-list server or an individual's email address.  
-
-Log in as a system administrator.  Navigate to the "Site Admin" table of contents
-(link in the right side of the header). Go to "Site Information" (under "Site 
-Configuration").  In the "Site Information Editing Form," enter a functional 
-email address in the field "Contact Email Address." and submit the change.
-
-If you set the Vitro.smtpHost in Step IV and do NOT provide an email address
-in this step, your users will receive a java error in the interface.
-
--------------------------------------------------------------------------------
-
-X. Set up Apache Tomcat Connector
-
-It is recommended that a Tomcat Connector such as mod_jk be used to ensure that 
-the site address does not include the port number (e.g. 8080) and an additional 
-reference to the Tomcat context name (e.g. /vivo).
-
-For example - http://example.com instead of http://example.com:8080/vivo
-
-Using the mod_jk connector allows for communication between Tomcat and the 
-primary web server. The "Quick Start HowTo" on the Apache site 
-http://tomcat.apache.org/connectors-doc/generic_howto/quick.html describes 
-the minimum server configurations for several popular web servers.
-
-After setting up the mod_jk connector above, you will need to modify the Tomcat's 
-server.xml ([tomcat root]/conf/) to respond to requests from Apache via the connector.
-
-Look for the  directive and add the following properties: 
-
-	connectionTimeout="20000" maxThreads="320" keepAliveTimeout="20000" 
-
-Note: the value for maxThreads (320) is equal to the value for MaxClients in the 
-httpd.conf file.
-
-Locate the  directive and update as follows:
-    
-
-	example.com
-	
-		
-		
-	
-
--------------------------------------------------------------------------------
- 
-XI. Configure Pellet Reasoner
-
-VIVO uses the Pellet engine to perform reasoning, which runs in the 
-background at startup and also when the knowledge base is edited. VIVO 
-continues serving pages while the reasoner continues working; when the
-reasoner finishes, the new inferences appear. Inferred statements are cached 
-in a database graph so that they are available immediately when VIVO is restarted.
-
-By default, Pellet is fed only an incomplete view of your ontology and only 
-certain inferences are materialized. These include rdf:type, 
-rdfs:subClassOf,owl:equivalentClass, and owl:disjointWith. This mode is 
-typically suitable for ontologies with a lot of instance data.  If you would 
-like to keep the default mode, skip to the next step.
-
-To enable "complete" OWL inference (materialize all significant entailed 
-statements), open "vitro-core/webapp/config/web.xml" and search for 
-PelletReasonerSetup.
-
-Then change the name of the listener class to PelletReasonerSetupComplete. 
-Because "complete" reasoning can be very resource intensive, there is also an 
-option to materialize nearly all inferences except owl:sameAs and 
-owl:differentFrom.
-
-This is enabled by specifying PelletReasonerSetupPseudocomplete. For ontologies 
-with large numbers of individuals, this mode can offer enormous performance 
-improvements over the "complete" mode.
-
-Finally, a class called PelletReasonerSetupPseudocompleteIgnoreDataproperties 
-is provided to improve performance on ontologies with large literals where data 
-property entailments are not needed.
-
--------------------------------------------------------------------------------
-
-XII. Using an External Authentication System with VIVO
-
-VIVO can be configured to work with an external authentication system like 
-Shibboleth or CUWebAuth.
-
-VIVO must be accessible only through an Apache HTTP server. The Apache server 
-will be configured to invoke the external authentication system. When the user 
-completes the authentication, the Apache server will pass a network ID to VIVO, 
-to identify the user.
-
-If VIVO has an account for that user, the user will be logged in with the 
-privileges of that account. In the absence of an account, VIVO will try to find 
-a page associated with the user. If such a page is found, the user can log in 
-to edit his own profile information.
-
----- Configuring the Apache server:
-
-Your institution will provide you with instructions for setting up the external 
-authentication system. The Apache server must be configured to secure a page in 
-VIVO. When a user reaches this secured page, the Apache server will invoke the 
-external authentication system.
-
-For VIVO, this secured page is named:
-    /loginExternalAuthReturn 
-When your instructions call for the location of the secured page, this is the 
-value you should use.
-
----- Configuring VIVO:
-
-To enable external authentication, VIVO requires three values in the 
-deploy.properties file.
-
-* The name of the HTTP header that will hold the external user’s network ID
-
-    When a user completes the authentication process, the Apache server will 
-    put the user’s network ID into one of the headers of the HTTP request. 
-    The instructions from your institution should tell you which header is 
-    used for this purpose. 
-
-    You need to tell VIVO the name of that HTTP header. Insert a line like 
-    this in the deploy.properties file:
-          externalAuth.netIdHeaderName = [the header name]
-    For example:
-          externalAuth.netIdHeaderName = remote_userID 
-
-* The text for the Login button
-
-    To start the authentication process, the user will click on a button in 
-    the VIVO login form. You need to tell VIVO what text should appear in that 
-    button.
-
-    Put a line like this in the deploy.properties file:
-          externalAuth.buttonText = [the text for your login button]
-    For example:
-          externalAuth.buttonText = Log in using BearCat Shibboleth
-          
-    The VIVO login form will display a button labelled “Log in using BearCat 
-    Shibboleth”.
-    
-* Associating a User with a profile page
-
-    If VIVO has an account for the user, the user will be given the privileges 
-    assigned to that account.
-     
-    In addition, VIVO will try to associate the user with a profile page, so 
-    the user may edit his own profile data. VIVO will search the data model 
-    for a person with a property that matches the User’s network ID.
-    
-    You need to tell VIVO what property should be used for matching. Insert 
-    a line like this in the deploy.properties file:
-          selfEditing.idMatchingProperty = [the URI of the property]
-    For example:
-          selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId
-
--------------------------------------------------------------------------------
-
-XIII. Was the installation successful?
-
-If you have completed the previous steps, you have good indications that the 
-installation was successful. 
-
-* Step VII showed that Tomcat recognized the webapp, and that the webapp was 
-    able to present the initial page.
-* Step VIII verified that you can log in to the administrator account.
-
-Here is a simple test to see whether the ontology files were loaded:
-* Click on the "Index" link on the upper left, below the logo. You should see
-    a "locations" section, with links for "Country" and "Geographic Location."
-    The index is built in a background thread, so on your first login, you may
-    see an empty index instead. Refresh the page periodically to see whether 
-    the index will be populated. This may take some time: with VIVO installed
-    on a modest laptop computer, loading the ontology files and building the 
-    index took more than 5 minutes from the time that Tomcat was started.
-* Click on the "Country" link. You should see an alphabetical list of the 
-    countries of the world.
-
-Here is a test to see whether your system is configured to serve linked data:
-* Point your browser to the home page of your website, and click the "Log in" link 
-    near the upper right corner. Log in with the initialAdminUser username you
-    set up in Step IV. If this is your first time logging in, you will be 
-    prompted to change the password.
-* After you have successfully logged in, click "site admin" in the upper right 
-	corner.  In the drop down under "Data Input" select "Faculty Member(core)"
-	and click the "Add individual of this class" button.
-* Enter the name "test individual" under the field "Individual Name," scroll to
-	the bottom, and click "Create New Record." You will be taken to the "Individual
-	Control Panel." Make note of the value of the field "URI" it will be used in 
-	the next step. 
-* Open a new web browser or browser tab to the page http://marbles.sourceforge.net/.
-  	In the pink box on that page enter the URI of the individual you created in the
-  	previous step and click "open."
-* In the resulting page search for the URI of the "test individual." You should 
-	find it towards the bottom of the page next to a red dot followed by "redirect 
-	(303)." This indicates that you are successfully serving linked RDF data.
-	If the URI of the "test individual" is followed by "failed (400)" you are not 
-	successfully serving linked data.
-     
-Finally, test the search index. 
-* The search box is on the right side, directly opposite the "Index" link.
-    Type the word "Australia" into the box, and click on the "Search" 
-    button.You should see a page of results, with links to countries that
-    border Australia, individuals that include Australia, and to 
-    Australia itself.


                 

                     
                 

                 

                     
                         Change the dbtype setting to use a database other than MySQL. 
-                        Otherwise, leave this value unchanged. 
-                        Possible values are DB2, derby, HSQLDB, H2, MySQL, Oracle,  
-                        PostgreSQL, and SQLServer. 
+                        Otherwise, leave this value unchanged.  
+                        Possible values are DB2, derby, HSQLDB, H2, MySQL, Oracle, 
+                        PostgreSQL, and SQLServer.  
                         Refer to http://openjena.org/wiki/SDB/Databases_Supported 
                         for additional information.
                     

                 

                     
-                        Specify a driver class name to use a database other than MySQL.
-                        Otherwise, leave this value unchanged. 
+                        Specify a driver class name to use a database other than MySQL. 
+                        Otherwise, leave this value unchanged.  
                         This JAR file for this driver must be added to the the 
                         webapp/lib directory within the vitro.core.dir specified above.