831 lines
39 KiB
HTML
831 lines
39 KiB
HTML
<!DOCTYPE HTML>
|
|
<html lang="en">
|
|
<head>
|
|
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
|
|
<meta charset="utf-8">
|
|
<title>VIVO Release 1 V1.4 Upgrade Guide</title>
|
|
<link rel="stylesheet" href="./css/doc.css" media="screen">
|
|
</head>
|
|
<body>
|
|
<div id="branding" role="banner">
|
|
<h1 class="vivo-logo"><a href="/"><span class="displace">VIVO</span></a></h1>
|
|
</div>
|
|
<!-- Start of content -->
|
|
<div id="wrapper-content" role="main">
|
|
<h1>VIVO Release 1 V1.4 Upgrade Guide</h1>
|
|
<small>
|
|
December 9, 2011 - Upgrading from Release 1 V1.3 to Release 1 V1.4
|
|
</small>
|
|
<toc>
|
|
<ul>
|
|
<li>
|
|
<a href="#announcement">Release announcement for V1.4</a>
|
|
</li>
|
|
<li>
|
|
<a href="#upgrade">Upgrade process for V1.4</a>
|
|
</li>
|
|
</ul>
|
|
</toc>
|
|
<p>
|
|
This document provides a short description of the steps involved in
|
|
upgrading your installation of VIVO from Version 1.3 to Version 1.4.
|
|
This and other documentation can be found on the <a href="http://vivoweb.org/support">support page</a>
|
|
at <a href="http://vivoweb.org/">VIVOweb.org</a>
|
|
</p>
|
|
<p>
|
|
If you need to do a fresh install, please consult the VIVO Release V1.4 Installation
|
|
Guide found on <a href="http://vivoweb.org/support">vivoweb.org</a>
|
|
or the install.html file located in the <code>doc</code>
|
|
directory of the VIVO source code distribution. The installation document also has a
|
|
list of the required software and versions (there are no new hardware
|
|
or software requirements for V1.4).
|
|
</p>
|
|
<h3 id="announcement">Release Announcement for V1.4</h3>
|
|
<!-- Release Announcement -->
|
|
<p><em>TBD</em></p>
|
|
<br>
|
|
|
|
<hr><!-- Page break --><!-- Upgrade process for V1.4 --><h2 id="upgrade">Upgrade process for V1.4</h2>
|
|
<toc>
|
|
<ol class="roman1">
|
|
<li>
|
|
<a href="#preparation">Before Performing the Upgrade</a>
|
|
</li>
|
|
<li>
|
|
<a href="#changes">Noteworthy Changes</a>
|
|
<br>
|
|
<ol class="roman2">
|
|
<li>
|
|
<a href="#template_changes">Template changes</a>
|
|
</li>
|
|
<li>
|
|
<a href="#proxy_editing">Profile editing by Proxies</a>
|
|
</li>
|
|
<li>
|
|
<a href="#tomcat_setup">Change to Tomcat configuration</a>
|
|
</li>
|
|
</ol>
|
|
</li>
|
|
<li>
|
|
<a href="#upgrade_process">The Upgrade Process</a>
|
|
</li>
|
|
<li>
|
|
<a href="#ontology">Ontology Changes</a>
|
|
<ol class="roman3">
|
|
<li>
|
|
<a href="#verify_ontology_upgrade">Verify
|
|
Ontology upgrade process</a>
|
|
</li>
|
|
<li>
|
|
<a href="#ontology_knowledge_base">Ontology
|
|
knowledge
|
|
base
|
|
manual review</a>
|
|
</li>
|
|
</ol>
|
|
</li>
|
|
<li>
|
|
<a href="#termsofuse">Review the VIVO Terms of Use</a>
|
|
</li>
|
|
</ol>
|
|
</toc>
|
|
|
|
<h3 id="preparation">I. Before Performing the Upgrade</h3>
|
|
<p>
|
|
Please ensure that backups are created of the:
|
|
</p>
|
|
<ul style="list-style-type: square;">
|
|
<li>
|
|
Tomcat webapps directory
|
|
</li>
|
|
<li>
|
|
Original source directory
|
|
</li>
|
|
<li>
|
|
MySQL database (mysqldump)
|
|
</li>
|
|
</ul>
|
|
<p>
|
|
The upgrade process is similar to the original install process
|
|
with
|
|
the following EXCEPTIONS:
|
|
</p>
|
|
<ul>
|
|
<li>
|
|
If you are still in RDB mode, it is required that you move
|
|
your
|
|
triple store to SDB while still at V1.2 (see <a href="#triple_store">Triple
|
|
Store</a>
|
|
info below).
|
|
<br>
|
|
</li>
|
|
<li>
|
|
DO NOT reinstall MySQL or recreate the MySQL database. Please
|
|
ensure that you back-up the MySQL database.
|
|
</li>
|
|
<li>
|
|
It is not necessary to add RDF data.
|
|
</li>
|
|
<li>
|
|
First-time login of the root account after the upgrade
|
|
process is complete will use the password previously set, NOT the
|
|
default password used on the first login after the initial
|
|
installation.
|
|
</li>
|
|
<li>
|
|
The first time Apache Tomcat starts up after the upgrade, it
|
|
will initiate a process that modifies the knowledge base to align the
|
|
data with the revised ontology. See the section on the <a href="#ontology">Ontology Upgrade</a>
|
|
below for more information.
|
|
</li>
|
|
</ul>
|
|
|
|
<h3 id="changes">II. Noteworthy Changes</h3>
|
|
|
|
<h4 id="template_changes">i. Template changes
|
|
</h4>
|
|
<ul>
|
|
<li><code>${stylesheets.list}</code>, <code>${scripts.list}</code>, and <code>${headscripts.list}</code> have changed to
|
|
<code>${stylesheets.list()}</code>, <code>${scripts.list()}</code>, and <code>${headscripts.list()}</code>, respectively.
|
|
</li>
|
|
(ryounes)
|
|
</ul>
|
|
|
|
<h4 id="proxy_editing">ii. Profile editing by Proxies
|
|
</h4>
|
|
<ul>
|
|
<li>addition to deploy.properties</li>
|
|
<li> What types of individuals may have proxy editors?
|
|
<pre>proxy.eligibleTypeList = http://xmlns.com/foaf/0.1/Person, http://xmlns.com/foaf/0.1/Organization</pre>
|
|
</li>
|
|
(jblake)
|
|
</ul>
|
|
|
|
<h4 id="tomcat_setup">iii. Change to Tomcat configuration
|
|
</h4>
|
|
<ul>
|
|
<li>Tomcat configuration</hli>
|
|
<li>Specify URI encoding
|
|
</li>
|
|
</ul>
|
|
(jblake)
|
|
|
|
<h3 id="upgrade_process">III. The Upgrade Process</h3>
|
|
<p>
|
|
1. Download the new distribution file and unpack it into a new
|
|
source directory.
|
|
</p>
|
|
<p>
|
|
2. Create a new deploy.properties using the same values as in
|
|
your
|
|
previous installation and set values for the new variables as described
|
|
below (vitro.local.solr.url, vitro.local.solr.ipaddress.mask,
|
|
vitro.home.directory, email.smptHost, email.replyTo,
|
|
rootUser.emailAddress)
|
|
<br>
|
|
</p>
|
|
<p>
|
|
<!-- deploy.properties table from install.html -->
|
|
</p>
|
|
<table border='1' bordercolor="#CCCCCC" cellspacing="5">
|
|
<tbody>
|
|
<tr>
|
|
<th>
|
|
Property Name
|
|
</th>
|
|
<th>
|
|
Example Value
|
|
</th>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
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 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/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/"<h5>* The namespace must end with "individual/" (including the
|
|
trailing slash).</h5>
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
Vitro.defaultNamespace
|
|
</td>
|
|
<td>
|
|
http://vivo.mydomain.edu/individual/
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
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).
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
vitro.core.dir
|
|
</td>
|
|
<td>
|
|
./vitro-core
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
Directory where tomcat is installed.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
tomcat.home
|
|
</td>
|
|
<td>
|
|
/usr/local/tomcat
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
Name of your VIVO application.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
webapp.name
|
|
</td>
|
|
<td>
|
|
vivo
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
URL of Solr context used in local VIVO search.
|
|
Should consist of:<pre> scheme + servername + port + vivo_webapp_name + "solr"</pre>
|
|
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"
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
vitro.local.solr.url
|
|
</td>
|
|
<td>
|
|
http://localhost:8080/vivosolr
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
Restricts access to the Solr search platform.
|
|
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.
|
|
<br>
|
|
Examples:<code>
|
|
<ul>
|
|
<li>
|
|
vitro.local.solr.ipaddress.mask = 127\.0\.0\.1
|
|
</li>
|
|
<li>
|
|
vitro.local.solr.ipaddress.mask =
|
|
127\.0\.0\.1,0:0:0:0:0:0:0:1
|
|
</li>
|
|
<li>
|
|
vitro.local.solr.ipaddress.mask = 169.254.*
|
|
</li>
|
|
</ul>
|
|
</code>
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
vitro.local.solr.ipaddress.mask
|
|
</td>
|
|
<td>
|
|
127\.0\.0\.1,0:0:0:0:0:0:0:1
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
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.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
vitro.home.directory
|
|
</td>
|
|
<td>
|
|
/usr/local/vivo/data
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
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.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
email.smtpHost
|
|
</td>
|
|
<td>
|
|
smtp.servername.edu
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
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.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
email.replyTo
|
|
</td>
|
|
<td>
|
|
vivoAdmin@my.domain.edu
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
Specify the JDBC URL of your database. Change
|
|
the end of the URL to reflect your database name (if it is not "vivo").
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
VitroConnection.DataSource.url
|
|
</td>
|
|
<td>
|
|
jdbc:mysql://localhost/vivo
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
Change the username to match the authorized user
|
|
you created in MySQL.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
VitroConnection.DataSource.username
|
|
</td>
|
|
<td>
|
|
username
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
Change the password to match the password you
|
|
created in MySQL.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
VitroConnection.DataSource.password
|
|
</td>
|
|
<td>
|
|
password
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
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.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
VitroConnection.DataSource.pool.maxActive
|
|
</td>
|
|
<td>
|
|
40
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
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.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
VitroConnection.DataSource.pool.maxIdle
|
|
</td>
|
|
<td>
|
|
10
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
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.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
VitroConnection.DataSource.dbtype
|
|
</td>
|
|
<td>
|
|
MySQL
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
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.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
VitroConnection.DataSource.driver
|
|
</td>
|
|
<td>
|
|
com.mysql.jdbc.Driver
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
Change the validation query used to test
|
|
database connections only if necessary to use a database other than
|
|
MySQL. Otherwise, leave this value unchanged.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
VitroConnection.DataSource.validationQuery
|
|
</td>
|
|
<td>
|
|
SELECT 1
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
Specify the email address of the root user
|
|
account for the VIVO application. This user will have an initial
|
|
temporary password of 'rootPassword'. You will be prompted to create a
|
|
new password on first login.
|
|
<p>
|
|
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.
|
|
</p>
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
rootUser.emailAddress
|
|
</td>
|
|
<td>
|
|
vivoAdmin@my.domain.edu
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
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).
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
selfEditing.idMatchingProperty
|
|
</td>
|
|
<td>
|
|
http://vivo.mydomain.edu/ns#networkId
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
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.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
externalAuth.buttonText
|
|
<br/>
|
|
externalAuth.netIdHeaderName
|
|
</td>
|
|
<td>
|
|
Log in using BearCat Shibboleth
|
|
<br/>
|
|
remote_userID
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
The temporal graph visualization can require
|
|
extensive machine resources. This can have a particularly noticable
|
|
impact on memory usage if
|
|
<ul>
|
|
<li>
|
|
The organization tree is deep,
|
|
</li>
|
|
<li>
|
|
The number of grants and publications is large.
|
|
</li>
|
|
</ul>
|
|
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.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
visualization.temporal
|
|
</td>
|
|
<td>
|
|
enabled
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
The temporal graph visualization is used to
|
|
compare different organizations/people within an organization on
|
|
parameters like number of publications or grants. By default, the app
|
|
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:
|
|
<br>
|
|
<code>visualization.topLevelOrg =
|
|
http://vivo.psm.edu/individual/n2862</code>
|
|
<br>
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
visualization.topLevelOrg
|
|
</td>
|
|
<td>
|
|
http://vivo-trunk.indiana.edu/individual/topLevelOrgURI
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
An absolute file path, pointing to the root directory of the Harvester utility.
|
|
You must include the final slash.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
harvester.location
|
|
</td>
|
|
<td>
|
|
/usr/local/vivo/harvester/
|
|
</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
|
|
<p>
|
|
3. Apply any previous changes you have made to the new source
|
|
directory.
|
|
</p>
|
|
<blockquote>
|
|
<strong>Special notes regarding source files</strong>
|
|
<ul>
|
|
<li>
|
|
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.
|
|
</li>
|
|
<li>
|
|
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.
|
|
</li>
|
|
<li>
|
|
NIH-funded VIVO implementations will need to apply the
|
|
Google
|
|
Analytics Tracking Code (GATC) to <code>googleAnalytics.ftl</code>
|
|
in
|
|
the theme:<pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre>
|
|
A sample <code>googleAnalytics.ftl</code>
|
|
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 of your institution's tracking code,
|
|
see the <a href="https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI">VIVO
|
|
Google
|
|
Analytics
|
|
wiki
|
|
page</a>.
|
|
</li>
|
|
</ul>
|
|
</blockquote>
|
|
<p>
|
|
4. If you had modified <code>web.xml</code>
|
|
to configure the
|
|
Pellet Reasoner (as described in the installation instructions), repeat
|
|
that modification.
|
|
</p>
|
|
<p>
|
|
5. Stop Apache Tomcat and from your VIVO source directory, run
|
|
ant
|
|
by typing: <code>ant all</code>
|
|
</p>
|
|
<p>
|
|
6. Start Apache Tomcat and log into VIVO as the root user when the upgrade is
|
|
completed. Depending on the size of your database, the migration process may
|
|
take up to several hours. When it is complete, you will
|
|
see a message in the catalina.log file that the server has started.<pre>INFO: Server startup in XXXXX ms</pre>
|
|
</p>
|
|
<p>
|
|
7. As root or an administrator, request a rebuild of the Solr search index:
|
|
Go to the "Site Admin" page and click on "Rebuild Search Index" under the
|
|
heading "Refresh Content".
|
|
</p>
|
|
<h3 id="ontology">IV. Ontology Changes</h3>
|
|
<h4 id="verify_ontology_upgrade">i. Verify Ontology upgrade process</h4>
|
|
<p>
|
|
After Apache Tomcat is started, these files should be reviewed to
|
|
verify that the automated upgrade process was executed
|
|
successfully. The ontology alignment process will create the
|
|
following files in the Tomcat <code>webapps/vivo/WEB-INF directory</code>:
|
|
</p>
|
|
<dl>
|
|
<dt>
|
|
<code>ontologies/update/logs/knowledgeBaseUpdate.(timestamp).log</code>
|
|
</dt>
|
|
<dd>
|
|
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 "Finished knowledge base migration". If this file contains any
|
|
warnings they should be reviewed with your implementation team
|
|
representative to see whether any corrective action needs to be taken.
|
|
</dd>
|
|
</dl>
|
|
<dl>
|
|
<dt>
|
|
<code>ontologies/update/logs/knowledgeBaseUpdate.(timestamp).error.log</code>
|
|
</dt>
|
|
<dd>
|
|
A log of errors that were encountered during the upgrade
|
|
process. This file should be empty if the upgrade was successful.
|
|
</dd>
|
|
</dl>
|
|
<dl>
|
|
<dt>
|
|
<code>ontologies/update/changedData/removedData.n3</code>
|
|
</dt>
|
|
<dd>
|
|
An N3 file containing all the statements that were removed
|
|
from
|
|
the knowledge base.
|
|
</dd>
|
|
</dl>
|
|
<dl>
|
|
<dt>
|
|
<code>ontologies/update/changedData/addedData.n3</code>
|
|
</dt>
|
|
<dd>
|
|
An N3 file containing all the statements that were added to
|
|
the
|
|
knowledge base.
|
|
</dd>
|
|
</dl>
|
|
<h4 id="ontology_knowledge_base">ii. Ontology knowledge base manual
|
|
review</h4>
|
|
<p>
|
|
Changes to the VIVO core ontology may require corresponding
|
|
modifications of the knowledge base instance data and local ontology
|
|
extensions.
|
|
</p>
|
|
<p>
|
|
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:
|
|
</p>
|
|
<dl>
|
|
<dt>
|
|
Class or Property renaming
|
|
</dt>
|
|
<dd>
|
|
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.
|
|
</dd>
|
|
</dl>
|
|
<dl>
|
|
<dt>
|
|
Class or Property deletion
|
|
</dt>
|
|
<dd>
|
|
All type assertions of a deleted class will be removed.
|
|
<br>
|
|
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.
|
|
</dd>
|
|
</dl>
|
|
<dl>
|
|
<dt>
|
|
Property addition
|
|
</dt>
|
|
<dd>
|
|
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.
|
|
</dd>
|
|
</dl>
|
|
<dl>
|
|
<dt>
|
|
Annotation property default values
|
|
</dt>
|
|
<dd>
|
|
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.
|
|
<br>
|
|
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.
|
|
</dd>
|
|
</dl>
|
|
<h3 id="termsofuse">V. Review the VIVO Terms of Use</h3>
|
|
<p>
|
|
VIVO comes with a "Terms of Use" statement linked from the footer. The "Site Name"
|
|
you assign in the "Site Information" form under the <strong>Site Admin</strong>
|
|
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:<pre>[vivo_source_dir]/vitro-core/webapp/web/templates/freemarker/body/termsOfUse.ftl</pre>
|
|
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.
|
|
</p>
|
|
<h3>Next Step ...</h3>
|
|
<p>
|
|
Now that you have VIVO up and running, please go read the <a href="http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Site_Administrator_Guide">Site Administrator's Guide</a>.
|
|
</p>
|
|
</div>
|
|
|
|
<!-- #wrapper-content -->
|
|
<div id="footer" role="contentinfo">
|
|
<p class="copyright">
|
|
<small>
|
|
©2011 All Rights Reserved
|
|
</small>
|
|
| Powered
|
|
by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a>
|
|
</p>
|
|
<div id="nav" role="navigation">
|
|
<ul id="footer-nav" role="list">
|
|
<li role="listitem">
|
|
<a href="http://vivoweb.org/about">About</a>
|
|
</li>
|
|
<li role="listitem">
|
|
<a href="http://vivoweb.org/contact">Contact Us</a>
|
|
</li>
|
|
<li role="listitem">
|
|
<a href="http://www.vivoweb.org/support" target="blank">Support</a>
|
|
</li>
|
|
</ul>
|
|
</div>
|
|
</div>
|
|
<!-- #footer -->
|
|
|
|
</div>
|
|
</body>
|
|
</html>
|