From 8275adc10f0c0a0b1ab8db0dce7fa15a01266eb8 Mon Sep 17 00:00:00 2001 From: briancaruso Date: Wed, 14 Dec 2011 22:20:23 +0000 Subject: [PATCH] Mergin 3856 3851 3838 3830 3829 3828 3827 from vivo 1.4 branch --- doc/install.html | 631 +++++++++++---------- doc/license.txt | 2 +- doc/list_view_configuration_guidelines.txt | 222 ++++++++ doc/release.html | 203 +++++++ doc/upgrades.html | 54 ++ flsdb2.deploy.properties | 119 ++++ large.deploy.properties | 119 ++++ productMods/semantic.cache | 15 + scripps.deploy.properties | 146 +++++ tomcat7.deploy.properties | 37 ++ vivo14.cornell.deploy.properites | 34 ++ vivoAi.deploy.properties | 118 ++++ vivojira.deploy.properties | 120 ++++ wcmcrdb.deploy.properties | 120 ++++ wcmcsdb.deploy.properties | 121 ++++ 15 files changed, 1749 insertions(+), 312 deletions(-) create mode 100644 doc/list_view_configuration_guidelines.txt create mode 100644 doc/release.html create mode 100644 doc/upgrades.html create mode 100644 flsdb2.deploy.properties create mode 100644 large.deploy.properties create mode 100644 productMods/semantic.cache create mode 100644 scripps.deploy.properties create mode 100644 tomcat7.deploy.properties create mode 100644 vivo14.cornell.deploy.properites create mode 100644 vivoAi.deploy.properties create mode 100644 vivojira.deploy.properties create mode 100644 wcmcrdb.deploy.properties create mode 100644 wcmcsdb.deploy.properties diff --git a/doc/install.html b/doc/install.html index bc284832..7b330d02 100644 --- a/doc/install.html +++ b/doc/install.html @@ -23,66 +23,66 @@ the VIVO v1.4 Release Announcement. This and other documentation can be found on the support - page at VIVOweb.org. + page at VIVOweb.org.

These instructions assume that you are performing a clean - install, including emptying an existing database, emptying the VIVO - home directory, 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. + install, including emptying an existing database, emptying the VIVO + home directory, 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.

- If you are going to upgrade an existing deployment, please consult - the Release 1 V1.4 Upgrade Guide in this directory. + If you are going to upgrade an existing service, please consult + the upgrade 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. + 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.

Where does VIVO live on your computer?

- Before beginning the installation, let's look at the four locations - on your computer that will hold VIVO. + Before beginning the installation, let's look at the four locations + on your computer that will hold VIVO.

The VIVO distribution directory

- This directory is created when you unpack the VIVO distribution file (see Step III, below). This directory is where you will + This is created when you unpack the VIVO distribution file (see Step III, below). This is where you will create your deploy.properties file (see Step - V, below), and where you will make any modifications to the VIVO - theme or code. You can create this directory wherever you choose. + V, below), and where you will make any modifications to the VIVO + theme or code. You can create this wherever you choose.

VIVO inside Tomcat

When you run the build script to compile and deploy VIVO (see Step VI, below), the files will be deployed to a - directory inside Tomcat. This is the actual executing code for VIVO, - but you won’t need to look at it or change it. If you need to change - VIVO, make the changes in the distribution directory, and run the build + directory inside Tomcat. This is the actual executing code for VIVO, + but you won’t need to look at it or change it. If you need to change + VIVO, make the changes in the distribution directory, and run the build script again. Tell the build script where to find Tomcat by setting tomcat.home in the deploy.properties file (see Step V, below).

The VIVO home directory

- VIVO will use this area to store some of the data it uses. Uploaded - image files are stored here, and the Solr home directory is stored here also. - You can create this wherever you choose. Tell VIVO where to find the + VIVO will use this area to store some of the data it uses. Uploaded + image files are stored here, and the Solr home directory is stored here also. + You can create this wherever you choose. Tell VIVO where to find the home directory by setting vitro.home.directory - in the deploy.properties file (see Step V, - below). You must create this directory before starting VIVO, and you - must ensure that Tomcat has permission to read and write to this - directory when it runs. + in the deploy.properties file (see Step V, + below). You must create this directory before starting VIVO, and you + must ensure that Tomcat has permission to read and write to this + directory when it runs.

The MySQL database

- The data that you add into VIVO will be stored in a MySQL database. The - actual location of this data depends on what - system you have, and on how you install MySQL (see Step I, below). - You will typically access the data through VIVO, or - occasionally through the MySQL client application. + Essentially all of the data that you store in VIVO will be given to + MySQL for storage. The actual location of this data depends on what + system you have, and on how you install MySQL (see Step I, below). but you won’t need to + know the location. You will access the data through VIVO, or + occasionally through the MySQL client application.

-

Installation Instructions

+

Steps to Installation

  1. Install required software @@ -113,7 +113,7 @@ using "Contact Us" form)
  2. - Set up Apache Tomcat Connector + Setup Apache Tomcat Connector
  3. Using an External Authentication @@ -129,13 +129,13 @@

    I. Install required software

    - Before installing VIVO, make sure that the following software is - installed on the desired machine: + Before installing VIVO, make sure that the following software is + installed on the desired machine:

    • Java (SE) 1.6.x* http://java.sun.com - (Not OpenJDK) + (Not OpenJDK)
    • Apache Tomcat 6.x or 7.x http://tomcat.apache.org @@ -150,77 +150,80 @@

      Be sure to set up 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 websites. + and add the executables to your path per + your operating system and installation directions from the software + support websites.

      - ** Note that from version V1.2 onward VIVO does - not support older versions of MySQL that - may have worked with 1.1.1. Be sure to use MySQL 5.1 or - higher. Using unsupported versions may result in strange error messages - related to table formatting or other unexpected problems. + * Note that vivo does not yet work with Java 1.7 +

      +

      + ** Note that from version V1.2 onward VIVO will does + not support older versions of MySQL that + may have worked with 1.1.1. Be sure to use MySQL 5.1 or + higher. Using unsupported versions may result in strange error messages + related to table formatting or other unexpected problems.

      II. Create an empty MySQL database

      - Decide on a database name, username, and password. Log into your + 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 + 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. + Most + of + the + time, the hostname will equal localhost. 

                      CREATE DATABASE dbname CHARACTER SET utf8;

      - Grant access to a database user. For example: + 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. + Keep track of the database name, username, and password for Step + IV.

      -

      III. Download the VIVO Application Source +

      III. Download the VIVO Application Source

      Download the VIVO application source as either rel-1.4.zip or rel-1.4.gz - file and unpack it on your web server: + file and unpack it on your web server:
      http://vivoweb.org/download

      IV. Specify deployment properties

      At the top level of the VIVO distribution directory, copy the file example.deploy.properties - to a file named simply deploy.properties. This file sets - several properties used in compilation and deployment. + 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 + 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 step below + 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 step below entitled Using an External Authentication - System with VIVO. + System with VIVO.

      @@ -231,98 +234,98 @@ the client. To make this possible, VIVO's default namespace must have a 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/" 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 + 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 + "http://www.example.edu/vivo/individual/"
      * The namespace must end with "individual/" (including the trailing slash).
      @@ -394,116 +397,117 @@ @@ -513,45 +517,45 @@ temporary password of 'rootPassword'. You will be prompted to create a new password on first login.

      - NOTE: The root user account has access to all data and all - operations in VIVO. Data views may be surprising when logged in as the - root user. It is best to create a Site Admin account to use for every - day administrative tasks. + NOTE: The root user account has access to all data and all + operations in VIVO. Data views may be surprising when logged in as the + root user. It is best to create a Site Admin account to use for every + day administrative tasks.

      @@ -563,7 +567,7 @@ @@ -573,22 +577,22 @@ impact on memory usage if
      • - The organization tree is deep, + The organization tree is deep,
      • - The number of grants and publications is large. + The number of grants and publications is large.
      - VIVO V1.4 mitigates this problem by the way of a caching - mechanism and hence we can safely set this to be enabled by default. + VIVO V1.4 mitigates this problem by the way of a caching + mechanism and hence we can safely set this to be enabled by default. @@ -599,10 +603,10 @@ will attempt to make its best guess at the top level organization in your instance. If you're unhappy with this selection, uncomment out the property below and set it to the URI of the organization individual you - want to identify as the top level organization. It will be used as the - default whenever the temporal graph visualization is rendered without - being passed an explicit org. For example, to use "Ponce School of - Medicine" as the top organization: + want to identify as the top level organization. It will be used as the + default whenever the temporal graph visualization is rendered without + being passed an explicit org. For example, to use "Ponce School of + Medicine" as the top organization:
      visualization.topLevelOrg = http://vivo.psm.edu/individual/n2862 @@ -611,10 +615,10 @@ @@ -625,10 +629,10 @@ @@ -651,33 +655,38 @@
      - Property Name + Property Name - Example Value + Example Value
      - Vitro.defaultNamespace + Vitro.defaultNamespace - http://vivo.mydomain.edu/individual/ + http://vivo.mydomain.edu/individual/
      - Directory where Vitro code is located. In most - deployments, this is set to ./vitro-core (It is not uncommon for this - setting to point elsewhere in development environments). + Directory where Vitro code is located. In most + deployments, this is set to ./vitro-core (It is not uncommon for this + setting to point elsewhere in development environments).
      - vitro.core.dir + vitro.core.dir - ./vitro-core + ./vitro-core
      - Directory where tomcat is installed. + Directory where tomcat is installed.
      - tomcat.home + tomcat.home - /usr/local/tomcat + /usr/local/tomcat
      - Name of your VIVO application. + Name of your VIVO application.
      - webapp.name + webapp.name - vivo + vivo
      URL of Solr context used in local VIVO search. Should consist of:
          scheme + servername + port + vivo_webapp_name + "solr"
      - In the standard installation, the Solr context will be on the same - server as VIVO, and in the same Tomcat instance. The path will be the - VIVO webapp.name (specified above) + "solr" + In the standard installation, the Solr context will be on the same + server as VIVO, and in the same Tomcat instance. The path will be the + VIVO webapp.name (specified above) + "solr"
      - vitro.local.solr.url + vitro.local.solr.url - http://localhost:8080/vivosolr + http://localhost:8080/vivosolr
      Restricts access to the Solr search platform. - The value is a regular expression. When a request is - made to Solr, the IP address of the requestor must the expression, - or the request will be rejected. + One or more regular expressions, separated by commas. When a request is + made to Solr, the IP address of the requestor must match one of the + patterns, or the request will be rejected.
      Examples:
      • - vitro.local.solr.ipaddress.mask = 127\.0\.0\.1 + vitro.local.solr.ipaddress.mask = 127\.0\.0\.1
      • - vitro.local.solr.ipaddress.mask = - 127\.0\.0\.1|0:0:0:0:0:0:0:1 + vitro.local.solr.ipaddress.mask = + 127\.0\.0\.1,0:0:0:0:0:0:0:1
      • - vitro.local.solr.ipaddress.mask = 169.254.* + vitro.local.solr.ipaddress.mask = 169.254.*
      @@ -330,60 +333,60 @@
      - vitro.local.solr.ipaddress.mask + vitro.local.solr.ipaddress.mask - 127\.0\.0\.1,0:0:0:0:0:0:0:1 + 127\.0\.0\.1,0:0:0:0:0:0:0:1
      - Directory where the VIVO application will store - the data that it creates. This includes uploaded files (usually images) - and the Solr search index. Be sure this directory exists and is - writable by the user who the Tomcat service is running as. + Directory where the VIVO application will store + the data that it creates. This includes uploaded files (usually images) + and the Solr search index. Be sure this directory exists and is + writable by the user who the Tomcat service is running as.
      - vitro.home.directory + vitro.home.directory - /usr/local/vivo/data + /usr/local/vivo/data
      - Specify an SMTP host that the application will - use for sending e-mail (Optional). If this is left blank, the contact - form will be hidden and disabled, and users will not be notified of - changes to their accounts. + Specify an SMTP host that the application will + use for sending e-mail (Optional). If this is left blank, the contact + form will be hidden and disabled, and users will not be notified of + changes to their accounts.
      - email.smtpHost + email.smtpHost - smtp.servername.edu + smtp.servername.edu
      Specify an email address which will appear as the sender in e-mail notifications to users (Optional). If a user - replies to the notification, this address will receive the reply. If a - user's e-mail address is invalid, this address will receive the error - notice. If this is left blank, users will not be notified of changes to - their accounts. + replies to the notification, this address will receive the reply. If a + user's e-mail address is invalid, this address will receive the error + notice. If this is left blank, users will not be notified of changes to + their accounts.
      - email.replyTo + email.replyTo - vivoAdmin@my.domain.edu + vivoAdmin@my.domain.edu
      - VitroConnection.DataSource.url + VitroConnection.DataSource.url - jdbc:mysql://localhost/vivo + jdbc:mysql://localhost/vivo
      - Change the username to match the authorized user - you created in MySQL. + Change the username to match the authorized user + you created in MySQL.
      - VitroConnection.DataSource.username + VitroConnection.DataSource.username - username + username
      - Change the password to match the password you - created in MySQL. + Change the password to match the password you + created in MySQL.
      - VitroConnection.DataSource.password + VitroConnection.DataSource.password - password + password
      - Specify the maximum number of active connections - in the database connection pool to support the anticipated number of - concurrent page requests. + 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.
      - VitroConnection.DataSource.pool.maxActive + VitroConnection.DataSource.pool.maxActive - 40 + 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. + 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.
      - VitroConnection.DataSource.pool.maxIdle + VitroConnection.DataSource.pool.maxIdle - 10 + 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. + 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.
      - VitroConnection.DataSource.dbtype + VitroConnection.DataSource.dbtype - MySQL + 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. + 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.
      - VitroConnection.DataSource.driver + VitroConnection.DataSource.driver - com.mysql.jdbc.Driver + 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. + Change the validation query used to test + database connections only if necessary to use a database other than + MySQL. Otherwise, leave this value unchanged.
      - VitroConnection.DataSource.validationQuery + VitroConnection.DataSource.validationQuery - SELECT 1 + SELECT 1
      - rootUser.emailAddress + rootUser.emailAddress - vivoAdmin@my.domain.edu + vivoAdmin@my.domain.edu
      - The URI 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 - (the value of the property must be either a String literal or an untyped literal). + The URI 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 + (the value of the property must be either a String literal or an untyped literal).
      - selfEditing.idMatchingProperty + selfEditing.idMatchingProperty - http://vivo.mydomain.edu/ns#networkId + http://vivo.mydomain.edu/ns#networkId
      - If an external authentication system like Shibboleth or CUWebAuth is to be - used, these properties say how the login button should be labeled, and which - HTTP header will contain the user ID from the authentication system. If such - a system is not to be used, leave these commented out. Consult the installation - instructions for more details. + If an external authentication system like Shibboleth or CUWebAuth is to be + used, these properties say how the login button should be labeled, and which + HTTP header will contain the user ID from the authentication system. If such + a system is not to be used, leave these commented out. Consult the installation + instructions for more details.
      Log in using BearCat Shibboleth
      - remote_userID + remote_userID
      - visualization.temporal + visualization.temporal - enabled + enabled
      - visualization.topLevelOrg + visualization.topLevelOrg - http://vivo-trunk.indiana.edu/individual/topLevelOrgURI + http://vivo-trunk.indiana.edu/individual/topLevelOrgURI
      - harvester.location + harvester.location - /usr/local/vivo/harvester/ + /usr/local/vivo/harvester/

      V. Compile and deploy

      - At the command line, from the top level of the VIVO distribution - directory, type: + At the command line, from the top level of the VIVO distribution + directory, type: 

                      ant all

      - to build VIVO and deploy to Tomcat's webapps directory. + to build VIVO and deploy to Tomcat's webapps directory.

      VI. Configure Tomcat

      Set JVM parameters

      - VIVO may 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 + VIVO copies small sections 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 may 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. If this file does not exist in Tomcat's bin directory, you can create it.
      - For example: + For example: 

                          export CATALINA_OPTS="-Xms512m -Xmx512m -XX:MaxPermSize=128m"

      This sets Tomcat to allocate an initial heap of 512 megabytes, a - maximum heap of 512 megabytes, and a PermGen space of 128 megs. Lower + maximum heap of 512 megabytes, and a PermGen space of 128 megs. Lower values may suffice, especially for small test installations.

      - 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.

      Set security limits

      @@ -691,12 +700,12 @@ 

                          apache	hard	nproc	400
                          tomcat6	hard	nproc	1500

      Set URI encoding

      - In order for VIVO to correctly handle international characters, - you must configure Tomcat to conform to the URI standard by + In order for VIVO on Tomcat to correctly handle for international characters, + you must configure Tomcat to conform to the URI standard by accepting percent-encoded UTF-8.

      - Edit Tomcat's conf/server.xml and add the following attribute to each of the + Edit Tomcat's conf/server.xml and add the following attribute to each of the Connector elements: URIEncoding="UTF-8". 

      @@ -722,7 +731,7 @@
                 from the overridden context fragment.
             
      
             
      
-                See Step X below,
+                See Step X below, 
                 for an example of overriding the VIVO context fragment.
             
      
 
@@ -730,14 +739,15 @@
             
      
                 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 (or the appropriate URL based on the webapp.name value in deploy.properties) to test the application.
+                browser to http://localhost:8080/vivo 
+                to test the application. 
             
      
             
      
                On start up VIVO will run some diagnostic tests. If a
-               problem is detected, the normal VIVO pages will redirect
+               problem is detected the normal VIVO pages will redirect
                to a startup status page describing the problem. You
                can stop tomcat, attempt to fix the problem and
-               proceed from Step V. The
+               proceeded from Step V. The
                startup status page may offer a continue link which
                will allow you to use VIVO inspite of the problems.
 
@@ -747,7 +757,7 @@
                 directory. Error messages are commonly found
                 in tomcat/logs/catalina.out
                 or tomcat/logs/vivo.all.log
-                or tomcat/logs/localhost.log.
+                or tomcat/logs/localhost.log
             
      
             
      VIII. Log in and add RDF data 
      
             
      
@@ -760,13 +770,13 @@
                 "rootPassword" (without the quotes). On first login,
                 you will be prompted to select a new password and
                 verify it a second time. When login is complete, the
-                search index is checked and, if it is empty, a full
-                index build will be triggered in the background in
+                search index is checked and, if it is empty, øa full
+                index build will be triggered in the background, in
                 order to ensure complete functionality throughout the
                 site.
             
      
             
      
-                After logging in, you can navigate to the "Site Admin" page that presents a menu of
+                After logging in, 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
@@ -778,126 +788,126 @@
                 ontologies from an RDF file.
             
      
             
      
-                Under the "Advanced Data Tools" section, click "Add/Remove RDF
+                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 the RDF data from a file on
+                RDF data you wish to load or upload from 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 right of
-                the page will show a simple index of the knowledge base.
+                Clicking the "Index" tab in the navigation bar at the top right of 
+                the page will show a simple index of the knowledge base. 
             
      
             
      
-                See more documentation for configuring VIVO, ingesting data, and
+                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 (email.smtpHost), you will also need to
-                add an email address to the VIVO application.  This is the email
-                to which the contact form will submit. It can be a list server or an
-                individual's email address.
+                feature in Step IV (email.smtpHost), you will also need to 
+                add an email address to the VIVO application.  This is the email 
+                to which the contact form will submit. 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.
+                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 email.smtpHost
-                in Step IV and do NOT
-                provide an email address in this step, your users will receive a java
-                error in the interface.
+                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).
+                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). 
             
      
             
      
-                This will make VIVO available at "http://example.com" instead of
-                "http://example.com:8080/vivo"
+                This will make VIVO available at "http://example.com" instead of 
+                "http://example.com:8080/vivo" 
             
      
             
      
-                Using the mod_jk connector allows for communication between Tomcat
+                Using the mod_jk connector allows for communication between Tomcat 
                 and the primary web server. The Quick
                     Start
                     HowTo
-                on the Apache site describes the minimum server
-                configurations for several popular web servers.
+                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
+                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:
+                respond 
+                to 
+                requests from Apache via the connector. Look for the  
+                <connector> directive and add the following properties: 
             
      
             
                      connectionTimeout="20000" maxThreads="320" keepAliveTimeout="20000"  
                  
      
             
      
-                Note: the value for maxThreads (320) is equal to the value for
+                Note: the value for maxThreads (320) is equal to the value for 
                 MaxClients in the apache's httpd.conf
-                file.
+                file. 
             
      
             
      
                 Locate the <Host name="localhost"...>
-                directive
-                and update as follows:
+                directive 
+                and update as follows: 
             
      
             
                    <Host name="localhost" appBase="webapps"
                        DeployOnStartup="false"
                        unpackWARs="true" autoDeploy="false"
                        xmlValidation="false" xmlNamespaceAware="false">
-
+                   
                    <Alias>example.com</Alias>
-
+                   
                    <Context path=""
                            docBase="/usr/local/tomcat/webapps/vivo"
                            reloadable="true"
                            cookies="true" >
-
+                   
                        <Manager pathname="" />
-
+                   
                        <Environment type="java.lang.String" override="false"
                                name="path.configuration"
                                value="deploy.properties"
                        />
                    </Context>
-
+                  
                    ...
             
      
 
-            
      XI. Using an External Authentication System
+            
      XI. Using an External Authentication System 
                 with VIVO 
      
             
      
             
      
             
      
-                VIVO can be configured to work with an external authentication
-                system like Shibboleth or CUWebAuth.
+                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.
+                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.
+                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
      
             
      
@@ -910,32 +920,32 @@
                 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.
+                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
+                To enable external authentication, VIVO requires three values in 
                 the deploy.properties
-                file.
+                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.
+                        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:
+                        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:
+                        For example: 
                     
        
                     
        externalAuth.netIdHeaderName = remote_userID
        
                 
        • 
@@ -950,8 +960,8 @@
                     
        
                     
        externalAuth.buttonText = Log in using BearCat Shibboleth
        
                     
        
-                        The VIVO login form will display a button labelled "Log in
-                        using BearCat Shibboleth".
+                        The VIVO login form will display a button labelled "Log in 
+                        using BearCat Shibboleth". 
                     
        
                 
                 
      • 
@@ -959,31 +969,31 @@
                     
        
                         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 (the value of the property must be either a String literal or an
-                        untyped literal). You need to tell VIVO what property should be used
-                        for matching. Insert a line like this in the deploy.properties file:
+                        data model for a person with a property that matches the User’s network 
+                        ID (the value of the property must be either a String literal or an 
+                        untyped literal). 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:
+                        For example: 
                     
        
                     
        selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId
        
                 
        • 
             
      
             
      XII. Was the installation successful? 
      
             
      
-                If you have completed the previous steps, you have good indications
-                that the installation was 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 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.
+                    Step VIII verified that you can log in to the administrator 
+                    account. 
                 
        • 
             
      
             
      
@@ -992,8 +1002,8 @@
               accessed from siteAdmin -> Startup status.
             
      
             
      
-                Here is a simple test to see whether the ontology files were
-                loaded:
+                Here is a simple test to see whether the ontology files were 
+                loaded: 
             
      
             
        
                 
      • 
@@ -1001,57 +1011,56 @@
                     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.
+                    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.
+                    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:
+                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
+                    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 rootUser.emailAddress
-                    you set up in Step IV. If this is your first time logging in, you will
-                    be prompted to change the password.
+                    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.
+                    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 word "Test" in the First Name field and the word "Individual" 
-                    in the Last Name field. Now, click the "Create Faculty Member" button. You 
-                    will be taken to the Profile page for the individual you just created. At
-                    the top of this page is the Admin Panel.  Make note of the "Resource URI" 
-                    value that is displayed here - it will be used in the next step.
+                    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 Resource URI of the test
+                    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.
+                    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.
+                Finally, test the search index. 
             
      
             
        
                 
      • 
@@ -1067,12 +1076,12 @@
             
      
             
      XIII. Review the VIVO Terms of Use
      
             
      
-                VIVO comes with a "Terms of Use" statement linked from the footer.
+                VIVO comes with a "Terms of Use" statement linked from the footer. 
                 The "Site Name" you assign in the "Site Information" form under the Site Admin
-                area will be inserted into the "Terms of Use"
-                statement.  If you want to edit the text content more than just  the
+                area will be inserted into the "Terms of Use" 
+                statement.  If you want to edit the text content more than just  the 
                 "Site Name", the file can be found here:
      [vivo_source_dir]/vitro-core/webapp/web/templates/freemarker/body/termsOfUse.ftl
      
-                Be sure to make the changes in your source files and deploy them to your
+                Be sure to make the changes in your source files and deploy them to your 
                 tomcat so you don't lose your changes next time you deploy for another reason.
             
      
             
      Next Step ...
      
@@ -1085,7 +1094,7 @@
             
      
               
                     All Rights Reserved see license
-                
+