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<!DOCTYPE html> <!DOCTYPE HTML>
<html lang="en"> <html lang="en">
<head> <head>
<meta http-equiv="content-type" content="text/html; charset=UTF-8"> <meta http-equiv="content-type" content="text/html; charset=UTF-8">
@ -12,9 +12,9 @@
</div> </div>
<!-- Start of content --> <!-- Start of content -->
<div id="wrapper-content" role="main"> <div id="wrapper-content" role="main">
<h1>VIVO Release 1 v1.3 Upgrade Guide</h1> <h1>VIVO Release 1 V1.3 Upgrade Guide</h1>
<small> <small>
July 22, 2011 - Upgrading from Release 1 v1.2 to Release 1 v1.3 July 28, 2011 - Upgrading from Release 1 V1.2 to Release 1 V1.3
</small> </small>
<toc> <toc>
<ul> <ul>
@ -33,77 +33,90 @@
at <a href="http://vivoweb.org/">VIVOweb.org</a> at <a href="http://vivoweb.org/">VIVOweb.org</a>
</p> </p>
<p> <p>
If you need to do a fresh install, please consult the VIVO Release If you need to do a fresh install, please consult the VIVO Release V1.3 Installation
1 v1.3 Installation Guide found on <a href="http://vivoweb.org/support">vivoweb.org</a> Guide found on <a href="http://vivoweb.org/support">vivoweb.org</a>
or the install.html file located in the <code>doc</code> or the install.html file located in the <code>doc</code>
directory of the VIVO source code distribution. The installation document also has a 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 list of the required software and versions (there are no new hardware
or software requirements for V1.3). or software requirements for V1.3).
</p> </p>
<h3 id="announcement">Release Announcement for V1.3</h3> <h3 id="announcement">Release Announcement for V1.3</h3>
V<!-- Release Announcement -->IVO Release 1.3 incorporates changes to <!-- Release Announcement -->VIVO Release V1.3 incorporates changes to the search
the search indexing, user accounts, menu management, ontology, and indexing, user accounts, menu management, ontology, and visualizations, and begins
visualizations. integration of VIVO Harvester functions with VIVO's own ingest tools.
<br> <br>
<h4>Search</h4> <h4>Search</h4>
VIVO 1.3 will feature notable improvements to the local search, <p>
primarily to improve relevance ranking but also to boost the influence VIVO V1.3 will feature notable improvements to the local search, primarily to improve relevance
of semantic relationships in the search. This will improve recall by ranking but also to boost the influence of semantic relationships in the search. This will
including text from related resources (e.g., adding a person&#39;s grant improve recall by including text from related resources (e.g., adding a person's grant and
and publication titles to his or her search entry) and by boosting publication titles to his or her search entry) and by boosting overall relevance ranking
overall relevance ranking based on the number and nature of connections based on the number and nature of connections from one individual to others.
from one individual to others. </p>
<br> <p>
VIVO is now using Apache Solr (http://lucene.apache.org/solr/) in place VIVO is now using Apache Solr (http://lucene.apache.org/solr/) in place of Apache Lucene to
of Apache Lucene to improve indexing and faceting of search results. improve indexing and faceting of search results. The migration to Solr also aligns the
The migration to Solr also aligns the local search with the VIVO local search with the VIVO multi-site search site under development for release prior to
multi-site search site under development for release prior to the 2011 the 2011 VIVO Conference.
VIVO Conference. </p>
<br>
<h4>Authorization</h4> <h4>Authorization</h4>
Release 1.3 provides an entirely new model of authorization within the <p>
VIVO application to allow more granular control over system Release V1.3 provides an entirely new model of authorization within the
configuration and editing. The first phase of the new user account VIVO application to allow more granular control over system
interface is included in V1.3. This interface provides a user search, a configuration and editing. The first phase of the new user account
root acount, and password reset functionality where the password gets interface is included in V1.3. This interface provides a user search, a
emailed to the user. The next phase will provide the ability to create root acount, and password reset functionality where the password gets
new roles. emailed to the user. The next phase will provide the ability to create
<br> new roles.
</p>
<h4>Menu management</h4> <h4>Menu management</h4>
The menus across the top of the site (Home, People, Organizations, <p>
Research, Events) can now be managed in a web form instead of editing The menus across the top of the site (Home, People, Organizations,
an RDF file. In addition to making site management much easier, Research, Events) can now be managed in a web form instead of editing
form-based editing also allows more control over what classes of data an RDF file. In addition to making site management much easier,
are displayed and provides a mechanism to limit certain menu pages to form-based editing also allows more control over what classes of data
content identified as internal to the institution. are displayed and provides a mechanism to limit certain menu pages to
<br> content identified as internal to the institution.
<h4>FreeMaker template improvements</h4> </p>
While less directly visible to the public, version 1.3 also includes <h4>FreeMarker template improvements</h4>
additional changes focused directly on supporting open source community <p>
involvement in extending and customizing VIVO. The development team While less directly visible to the public, V1.3 also includes
began a year ago to transition VIVO&#39;s code base away from Java Server additional changes focused directly on supporting open source community
Pages to the FreeMarker page templating system that much more cleanly involvement in extending and customizing VIVO. The development team
separates internal application programming logic from page display. began a year ago to transition VIVO&#39;s code base away from Java Server
<br> Pages to the FreeMarker page templating system that much more cleanly
separates internal application programming logic from page display.
</p>
<h4>Visualization</h4> <h4>Visualization</h4>
The visualization team has implemented a Map of Science visualization, <p>
which allows users to visually explore the scientific strengths of a The visualization team has implemented a Map of Science visualization,
university, school, department, or person in the VIVO instance. Users which allows users to visually explore the scientific strengths of a
will be able to see where an organization or person&#39;s interests lay university, school, department, or person in the VIVO instance. Users
across 13 major scientific disciplines or 554 sub-disciplines, and will will be able to see where an organization or person&#39;s interests lay
be able to see how these disciplines and sub-disciplines interrelate across 13 major scientific disciplines or 554 sub-disciplines, and will
with one another on the map of science. Wireframes and design be able to see how these disciplines and sub-disciplines interrelate
documentation for upcoming enhanced versions of the Map of Science with one another on the Map of Science. Wireframes and design
visualization have already been developed; the Map of Science documentation for upcoming enhanced versions of the Map of Science
visualization will most likely be in the form of a PDF that a user can visualization have already been developed; the Map of Science
download. visualization will most likely be in the form of a PDF that a user can
<br> download.
Several visualization also now provide a caching feature that improves </p>
performance after the initial processing. <p>
<br> Several visualizations also now provide a caching feature that improves
performance after the initial processing.
</p>
<h4>QR Codes</h4> <h4>QR Codes</h4>
Pages for people in VIVO have the option of displaying QR codes. <p>
<br> Pages for people in VIVO now have an icon for displaying QR codes to allow
capturing names and available contact information on mobile devices.
</p>
<h4>Harvester Integration</h4>
<p>
VIVO sites have the option with Release 1.3 of coordinating the configuration
of VIVO and the Harvester to enable many Harvester functions to be initiated
from the VIVO Ingest Tools menu in support of more unified and centralized
management for data ingest.
</p>
<h4>Ontology changes</h4> <h4>Ontology changes</h4>
<ul> <ul>
<li> <li>
@ -127,11 +140,12 @@
</li> </li>
</ul> </ul>
<h4>Linked open data</h4> <h4>Linked open data</h4>
Responses to linked data requests have been enhanced to include <p>
additional context about any individual, in working toward a goal of Responses to linked data requests have been enhanced to include
being able to provide all the data in a person's profile available as additional context about any individual, in working toward a goal of
RDF via a single web request. being able to provide all the data in a person's profile available as
<br> RDF via a single web request.
</p>
<br> <br>
<hr><!-- Page break --><!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.3</h2> <hr><!-- Page break --><!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.3</h2>
<toc> <toc>
@ -164,20 +178,23 @@
<a href="#upgrade_process">The Upgrade Process</a> <a href="#upgrade_process">The Upgrade Process</a>
</li> </li>
<li> <li>
<a href="upgrade-1.3.html#ontology">Ontology</a> <a href="#ontology">Ontology Changes</a>
<ol class="roman3"> <ol class="roman3">
<li> <li>
<a href="upgrade-1.3.html#verify_ontology_upgrade">Verify <a href="#verify_ontology_upgrade">Verify
Ontology upgrade process</a> Ontology upgrade process</a>
</li> </li>
<li> <li>
<a href="upgrade-1.3.html#ontology_knowledge_base">Ontology <a href="#ontology_knowledge_base">Ontology
knowledge knowledge
base base
manual review</a> manual review</a>
</li> </li>
</ol> </ol>
</li> </li>
<li>
<a href="#termsofuse">Review the VIVO Terms of Use</a>
</li>
</ol> </ol>
<h3 id="preparation">I. Before Performing the Upgrade</h3> <h3 id="preparation">I. Before Performing the Upgrade</h3>
<p> <p>
@ -209,22 +226,22 @@
<br> <br>
</li> </li>
<li> <li>
DO NOT reinstall MySQL or recreate the MySQL database. Please DO NOT reinstall MySQL or recreate the MySQL database. Please
ensure that you back-up the MySQL database. Also note that VIVO 1.2 ensure that you back-up the MySQL database. Also note that VIVO 1.2
will not run on older versions of MySQL that may have worked with will not run on older versions of MySQL that may have worked with
1.1.1. Be sure to run VIVO 1.2 with MySQL 5.1 or higher. Using 1.1.1. Be sure to run VIVO 1.2 with MySQL 5.1 or higher. Using
unsupported versions may result in strange error messages related to unsupported versions may result in strange error messages related to
table formatting or other unexpected problems. table formatting or other unexpected problems.
</li> </li>
<li> <li>
It is not necessary to add RDF data. It is not necessary to add RDF data.
</li> </li>
<li> <li>
First-time login of the administrator account after the First-time login of the administrator account after the
upgrade upgrade
process is complete will use the password previously set, NOT the process is complete will use the password previously set, NOT the
default password used on the first login after the initial default password used on the first login after the initial
installation. With V1.3 there is also a new root user. Please see the installation. With V1.3 there is also a new root user. Please see the
section on <a href="#authorization">Authorization changes</a> section on <a href="#authorization">Authorization changes</a>
for more for more
information. information.
@ -236,16 +253,15 @@
below for more information. below for more information.
</li> </li>
</ul> </ul>
<h3 id="changes">II. Noteworthy Changes <h3 id="changes">II. Noteworthy Changes</h3>
</h3> <h4 id="triple_store">i. Triple store
<h4 id="triple_store">i. Triple store changes
<br> <br>
</h4> </h4>
<p> <p>
VIVO 1.3 now requires you to use Jena's SPARQL database (SDB) for VIVO 1.3 now requires you to use Jena's SPARQL database (SDB) for
the triple store technology.&nbsp; Jena's legacy relational database the triple store technology.&nbsp; Jena's legacy relational database
store (RDB) was used by VIVO 1.1.1 and earlier.&nbsp; Both SDB and RDB store (RDB) was used by VIVO 1.1.1 and earlier.&nbsp; Both SDB and RDB
were available in VIVO 1.2 and 1.2.1.&nbsp; It is required that you were available in VIVO 1.2 and 1.2.1.&nbsp; It is required that you
move your triple store to SDB while still at V1.2. move your triple store to SDB while still at V1.2.
</p> </p>
<p> <p>
@ -254,26 +270,26 @@
allows VIVO installations to display data from large RDF models while allows VIVO installations to display data from large RDF models while
requiring only a small amount of server memory to run the application. requiring only a small amount of server memory to run the application.
There is a tradeoff in response time: pages may take slightly longer to There is a tradeoff in response time: pages may take slightly longer to
load in SDB mode, and performance will depend on the configuration load in SDB mode, and performance will depend on the configuration
parameters of the database server. Additionally, advanced OWL reasoning parameters of the database server. Additionally, advanced OWL reasoning
(not enabled by default in either mode) is not possible in SDB mode. (not enabled by default in either mode) is not possible in SDB mode.
With SDB, only the default set of inferences (inferred rdf:type With SDB, only the default set of inferences (inferred rdf:type
statements) are generated, and they are generated as soon as data is statements) are generated, and they are generated as soon as data is
edited rather than in a background process. edited rather than in a background process.
</p> </p>
<p> <p>
A conversion from RDB to SDB mode can take a number of hours to A conversion from RDB to SDB mode can take a number of hours to
complete if the installation contains a large amount of RDF data complete if the installation contains a large amount of RDF data
(roughly a million triples or more).&nbsp; You can start the conversion (roughly a million triples or more).&nbsp; You can start the conversion
process in the background while the RDB system is running. This will process in the background while the RDB system is running. This will
reduce the delay in initial startup after the application is redeployed reduce the delay in initial startup after the application is redeployed
with deploy.properties set for SDB. <span style="font-weight: bold;">Note with deploy.properties set for SDB. <span style="font-weight: bold;">Note
that it is important not to edit any data anywhere in the application that it is important not to edit any data anywhere in the application
while this background conversion is running</span>. while this background conversion is running</span>.
</p> </p>
<p> <p>
To start the SDB conversion, log in as a system administrator and To start the SDB conversion, log in as a system administrator and
request /sdbsetup (For example, if your VIVO is installed at request /sdbsetup (for example, if your VIVO is installed at
http://vivo.myuniversity.edu/ you would type http://vivo.myuniversity.edu/ you would type
http://vivo.myuniversity.edu/sdbsetup into your browser). http://vivo.myuniversity.edu/sdbsetup into your browser).
</p> </p>
@ -283,37 +299,35 @@
<p> <p>
During the course of the SDB setup, which may take several hours During the course of the SDB setup, which may take several hours
on on
a large database, subsequent requests to /sdbsetup will display a a large database, subsequent requests to /sdbsetup will display a
message that the operation is still in progress. When a request for message that the operation is still in progress. When a request for
this page shows a message that the SDB setup has completed this page shows a message that the SDB setup has completed
successfully, shut down Tomcat, set deploy.properties to SDB mode, successfully, shut down Tomcat, set deploy.properties to SDB mode,
redeploy, and restart Tomcat. VIVO will now be running from the SDB redeploy, and restart Tomcat. VIVO will now be running from the SDB
store. store.
</p> </p>
<p> <p>
</p> </p>
<h4 id="theme">ii. Theme changes</h4> <h4 id="theme">ii. Theme</h4>
<p> <p>
The vivo-basic theme was deprecated with VIVO V1.2 and is no longer The vivo-basic theme was deprecated with VIVO V1.2 and is no longer
present in the V1.3 release as it does not support V1.2 or V1.3 present in the V1.3 release as it does not support V1.2 or V1.3
features. It is highly recommended that you use the wilma theme or features. It is highly recommended that you use the wilma theme or
modify the wilma theme for branding or to create a custom look and modify the wilma theme for branding or to create a custom look and
feel. Please see the <a href="http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Site_Administrator_Guide">Site Administration Guide</a> feel. Please see the <a href="http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Site_Administrator_Guide">Site Administration Guide</a>
for more information about customizing your for more information about customizing your
theme. theme.
</p> </p>
</toc> </toc>
<h4 id="template">iii. Template changes</h4> <h4 id="template">iii. Template</h4>
<toc> <toc>
<ul> <ul>
<li> <li>
<p> <p>
The <code>${stylesheets}</code>, <code>${scripts}</code>, The <code>${stylesheets}</code>, <code>${scripts}</code>,
and<code>${headScripts}</code> and <code>${headScripts} add()</code>
<code>add()</code> methods now take the full tag as an argument.
methods now take the This will require a change to all calls to these methods in the
full tag as an argument.
This will require a change to all calls to these methods in the
templates. This change allows for specification of attributes such as <code>media</code> templates. This change allows for specification of attributes such as <code>media</code>
directly in the tag. For example: directly in the tag. For example:
</p> </p>
@ -333,8 +347,8 @@
</li> </li>
<li> <li>
The <code>addFromTheme()</code> The <code>addFromTheme()</code>
methods of the <code>${stylesheets}</code>,<code>${scripts}</code>, methods of the <code>${stylesheets}</code>, <code>${scripts}</code>,
and<code>${headScripts}</code> and <code>${headScripts}</code>
objects have been deleted. Substitute as objects have been deleted. Substitute as
shown in the preceding example. shown in the preceding example.
</li> </li>
@ -346,7 +360,7 @@
</li> </li>
</ul> </ul>
</toc> </toc>
<h4 id="listview">v. List view changes</h4> <h4 id="listview">v. List view</h4>
<toc> <toc>
<code>&lt;query-base&gt;</code> <code>&lt;query-base&gt;</code>
and <code>&lt;query-collated&gt;</code> and <code>&lt;query-collated&gt;</code>
@ -356,20 +370,19 @@
<br> <br>
<br> <br>
</toc> </toc>
<h4 id="authorization">v. Authorization changes</h4> <h4 id="authorization">v. Authorization</h4>
<toc> <toc>
<p> <p>
In release 1.3, the VIVO authorization system has some extensive In V1.3, the VIVO authorization system has some extensive
changes. In summary, these are: changes. In summary, these are:
</p> </p>
<ul> <ul>
<li> <li>
Each user will have a user account, even if the user logs in Each user will have a user account, even if the user logs in
by with Shibboleth or some other external authentication system.
Shibboleth or some other external authentication system.
</li> </li>
<li> <li>
E-mail is used to notify user's when an account is created for E-mail is used to notify users when an account is created for
them, or when an administrator edits their account. them, or when an administrator edits their account.
</li> </li>
<li> <li>
@ -385,33 +398,28 @@
<dl> <dl>
<dd> <dd>
<p style="margin-left: 40px;"> <p style="margin-left: 40px;">
With release 1.3, each authenticated With V1.3, each authenticated user will have a user
user will have a user
account. If someone logs in using an external authentication system, account. If someone logs in using an external authentication system,
and no user account matches their external login credentials, an and no user account matches their external login credentials, an
account will be created. account will be created.
</p> </p>
<p style="margin-left: 40px;"> <p style="margin-left: 40px;">
The user will be prompted to enter The user will be prompted to enter information for the
information for the account being created: first name, last name, and e-mail address.
account
being created: first name, last name, and e-mail address.
</p> </p>
</dd> </dd>
</dl> </dl>
</toc> </toc>
<toc> <toc>
<h4 style="margin-left: 40px;" id="email_on_accounts">b. E-mail address <h4 style="margin-left: 40px;" id="email_on_accounts">b. E-mail address
becomes an important becomes an important part of User Accounts</h4>
part
of User Accounts</h4>
<dl style="margin-left: 40px;"> <dl style="margin-left: 40px;">
<dd> <dd>
<p> <p>
Prior to release 1.3, each user account was identified by a Prior to V1.3, each user account was identified by a
Username field. This field was labeled as &quot;E-mail address&quot; on some Username field. This field was labeled as &quot;E-mail address&quot; on some
pages in VIVO, but no mail was ever sent. In release 1.3, this has pages in VIVO, but no mail was ever sent. In V1.3, this has
changed, so the e-mail address is fully used, both for identification changed, so the e-mail address is fully used, both for identification
and for communication with the user. and for communication with the user.
</p> </p>
</dd> </dd>
@ -426,54 +434,48 @@
<dl style="margin-left: 40px;"> <dl style="margin-left: 40px;">
<dd> <dd>
<p> <p>
Prior to release 1.3, the Username field (also referred to as Prior to V1.3, the Username field (also referred to as
'e-mail address') was used for several purposes: 'e-mail address') was used for several purposes:
</p> </p>
<ul> <ul>
<li> <li>
Idenfiying the user account. Idenfiying the user account
</li> </li>
<li> <li>
Part of the user&#39;s credentials when logging in (along with Part of the user&#39;s credentials when logging in (along with
a a password)
password).
</li> </li>
<li> <li>
Connecting the user account to an external authentication Connecting the user account to an external authentication
system, like Shibboleth or CUWebAuth. system, like Shibboleth or CUWebAuth
</li> </li>
<li> <li>
Connecting the user account to a personal Profile page. Connecting the user account to a personal Profile page
</li> </li>
</ul> </ul>
<p> <p>
With release 1.3, these functions are handled by two separate With V1.3, these functions are handled by two separate
fields called EmailAddress field and ExternalAuthId. fields called EmailAddress field and ExternalAuthId.
</p> </p>
<ul> <ul>
<li> <li>
EmailAddress is used when logging in (along with a EmailAddress is used when logging in (along with a
password). password)
</li> </li>
<li> <li>
EmailAddress is used to send notifications to the user EmailAddress is used to send notifications to the user
about about changes to his/her account (see below)
changes to his/her account (see below).
</li> </li>
<li> <li>
The ExternalAuthId is used when logging in using an The ExternalAuthId is used when logging in using an
external external authentication system
authentication system.
</li> </li>
<li> <li>
The ExternalAuthId is used to connect the user account to The ExternalAuthId is used to connect the user account to
a a personal Profile page
personal Profile page.
<blockquote> <blockquote>
<strong>Note:</strong> <strong>Note:</strong>
With release 1.3, the With V1.3, the ExternalAuthId can now be matched against either an untyped literal or a string literal in the Profile page.
ExternalAuthId can now be matched against either an untyped literal or
a string literal in the Profile page.
</blockquote> </blockquote>
</li> </li>
</ul> </ul>
@ -494,24 +496,24 @@
<dl style="margin-left: 40px;"> <dl style="margin-left: 40px;">
<dd> <dd>
<p> <p>
If you are upgrading to VIVO release 1.3 from an existing If you are upgrading to VIVO V1.3 from an existing
VIVO VIVO
installation, the user accounts in your system will be migrated into installation, the user accounts in your system will be migrated into
the new data structures. When migrating an account, both the the new data structures. When migrating an account, both the
EmailAddress field and the ExternalAuthId field will be set to the EmailAddress field and the ExternalAuthId field will be set to the
value of the Username field in the old account. The new account should value of the Username field in the old account. The new account should
behave as the old account did. behave as the old account did.
</p> </p>
<p> <p>
When creating a new user account, or editing an existing one, When creating a new user account, or editing an existing one,
the system requires that your e-mail address be in a valid form, like <code>somebody@somewhere.edu</code>. the system requires that your e-mail address be in a valid form, like <code>somebody@somewhere.edu</code>.
You You
should should
plan plan
for for
this this
as as
part of your migration to release 1.3 part of your migration to V1.3
</p> </p>
</dd> </dd>
</dl> </dl>
@ -526,7 +528,7 @@
<dl style="margin-left: 40px;"> <dl style="margin-left: 40px;">
<dd> <dd>
<p> <p>
With release 1.3, VIVO users receive e-mail notifications With V1.3, VIVO users receive e-mail notifications
when when
an account is created or modified for them or by them. an account is created or modified for them or by them.
</p> </p>
@ -538,11 +540,11 @@
</p> </p>
<blockquote> <blockquote>
<strong>Note:</strong> <strong>Note:</strong>
when creating the account, when creating the account,
the the
administrator may indicate that it will only be used with an external administrator may indicate that it will only be used with an external
authentication system like Shibboleth or CUWebAuth. In this case, the authentication system like Shibboleth or CUWebAuth. In this case, the
account will not require a password, and the e-mail notification account will not require a password, and the e-mail notification
message to the user will not provide a password link. message to the user will not provide a password link.
</blockquote> </blockquote>
<p> <p>
@ -565,15 +567,15 @@
</toc> </toc>
<div style="margin-left: 40px;"> <div style="margin-left: 40px;">
<toc> <toc>
<h5 style="margin-left: 40px;">4. Disabling e-mail notificiation</h5> <h5 style="margin-left: 40px;">4. Disabling e-mail notification</h5>
</toc> </toc>
</div> </div>
<toc> <toc>
<dl style="margin-left: 40px;"> <dl style="margin-left: 40px;">
<dd> <dd>
<p> <p>
The e-mail notification relies on two configuration The e-mail notification relies on two configuration
properties:<code>email.smtpHost</code> properties: <code>email.smtpHost</code>
and <code>email.replyTo</code>. If either of these properties is and <code>email.replyTo</code>. If either of these properties is
missing or empty, VIVO will not attempt to send e-mail notifications to missing or empty, VIVO will not attempt to send e-mail notifications to
users. users.
@ -584,9 +586,9 @@
</p> </p>
<p> <p>
If e-mail notifications are disabled, an administrator must If e-mail notifications are disabled, an administrator must
set set
a password on each new account, since the user will have no way of a password on each new account, since the user will have no way of
setting it. When the user logs in for the first time, VIVO will require setting it. When the user logs in for the first time, VIVO will require
them to change their password to one of their own choosing. them to change their password to one of their own choosing.
</p> </p>
</dd> </dd>
@ -597,10 +599,10 @@
<dl> <dl>
<dd> <dd>
<p style="margin-left: 40px;"> <p style="margin-left: 40px;">
Prior to release 1.3, each VIVO Prior to V1.3, each VIVO
installation was created with installation was created with
a a
default administrator&#39;s account. In release 1.3, there is no such default administrator&#39;s account. In V1.3, there is no such
account. Instead, each VIVO installation will have a &quot;root&quot; account. account. Instead, each VIVO installation will have a &quot;root&quot; account.
</p> </p>
<p style="margin-left: 40px;"> <p style="margin-left: 40px;">
@ -613,34 +615,34 @@
The password for this account is The password for this account is
automatically set to <code>rootPassword</code>, automatically set to <code>rootPassword</code>,
but but
you you
will will
be be
required required
to change the password the first time you log to change the password the first time you log
in. in.
</div> </div>
<blockquote style="margin-left: 40px;"> <blockquote style="margin-left: 40px;">
<strong>Note:</strong> <strong>Note:</strong>
the<code>initialAdminUser</code> the <code>initialAdminUser</code>
is no longer use. is no longer use.
</blockquote> </blockquote>
<p style="margin-left: 40px;"> <p style="margin-left: 40px;">
The root account is not a site The root account is not a site
administrator&#39;s account &mdash; it administrator&#39;s account &mdash; it
is is
more powerful than a site administrator&#39;s acocunt. The root account is more powerful than a site administrator&#39;s account. The root account is
permitted to visit any page in a VIVO application. It is permitted to permitted to visit any page in a VIVO application. It is permitted to
see any data property, and to enter data into any field. As such, the see any data property, and to enter data into any field. As such, the
root account can be very useful and rather dangerous. It can also give root account can be very useful and rather dangerous. It can also give
you a distorted view of what your VIVO site looks like, since data is you a distorted view of what your VIVO site looks like, since data is
shown which other accounts cannot see. shown here which ins not visible to other accounts.
</p> </p>
<p style="margin-left: 40px;"> <p style="margin-left: 40px;">
The root account is not intended for The root account is not intended for
routine, every day use. routine, everyday use.
The best way to use the root account is to create a site The best way to use the root account is to create a site
administrator&#39;s account. After that, use the root account only when administrator&#39;s account. After that, use the root account only when
necessary. necessary.
</p> </p>
</dd> </dd>
@ -651,11 +653,11 @@
source directory. source directory.
</p> </p>
<p> <p>
2. Create a new deploy.properties using the same values as in 2. Create a new deploy.properties using the same values as in
your your
previous installation and set values for the new variables as described previous installation and set values for the new variables as described
below (vitro.local.solr.url, vitro.local.solr.ipaddress.mask, below (vitro.local.solr.url, vitro.local.solr.ipaddress.mask,
vitro.home.directory, email.smptHost, email.replyTo, vitro.home.directory, email.smptHost, email.replyTo,
rootUser.emailAddress) rootUser.emailAddress)
<br> <br>
</p> </p>
@ -762,20 +764,19 @@
made to Solr, the IP address of the requestor must match one of the made to Solr, the IP address of the requestor must match one of the
patterns, or the request will be rejected. patterns, or the request will be rejected.
<br> <br>
Examples: Examples:<code>
<code> <ul>
<ul> <li>
<li> vitro.local.solr.ipaddress.mask = 127\.0\.0\.1
vitro.local.solr.ipaddress.mask = 127\.0\.0\.1 </li>
</li> <li>
<li> 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 </li>
</li> <li>
<li> vitro.local.solr.ipaddress.mask = 169.254.*
vitro.local.solr.ipaddress.mask = 169.254.* </li>
</li> </ul>
</ul>
</code> </code>
</td> </td>
</tr> </tr>
@ -790,9 +791,9 @@
<tr> <tr>
<td colspan="2"> <td colspan="2">
Directory where the VIVO application will Directory where the VIVO application will
store store
the data that it creates. This includes uploaded files (usually images) the data that it creates. This includes uploaded files (usually images)
and the Solr search index. Be sure this directory exists and is and the Solr search index. Be sure this directory exists and is
writable by the user who the Tomcat service is running as. writable by the user who the Tomcat service is running as.
</td> </td>
</tr> </tr>
@ -822,11 +823,11 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Specify an email address which will appear as Specify an email address which will appear as
the sender in e-mail notifications to users (Optional). If a user the sender in e-mail notifications to users (Optional). If a user
replies to the notification, this address will receive the reply. If a 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 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 notice. If this is left blank, users will not be notified of changes to
their accounts. their accounts.
</td> </td>
</tr> </tr>
@ -884,9 +885,9 @@
<tr> <tr>
<td colspan="2"> <td colspan="2">
Specify the Jena triple store technology to Specify the Jena triple store technology to
use. use.
SDB is Jena's SPARQL database; this setting allows RDF data to scale 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 beyond the limits of the JVM heap. Set to RDB to use the older Jena RDB
store with in-memory caching. store with in-memory caching.
</td> </td>
</tr> </tr>
@ -901,9 +902,9 @@
<tr> <tr>
<td colspan="2"> <td colspan="2">
Specify the maximum number of active Specify the maximum number of active
connections connections
in the database connection pool to support the anticipated number of in the database connection pool to support the anticipated number of
concurrent page requests. It is not necessary to adjust this value when concurrent page requests. It is not necessary to adjust this value when
using the RDB configuration. using the RDB configuration.
</td> </td>
</tr> </tr>
@ -933,9 +934,9 @@
<tr> <tr>
<td colspan="2"> <td colspan="2">
Change the dbtype setting to use a database Change the dbtype setting to use a database
other than MySQL. Otherwise, leave this value unchanged. Possible other than MySQL. Otherwise, leave this value unchanged. Possible
values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and
SQLServer. Refer to http://openjena.org/wiki/SDB/Databases_Supported SQLServer. Refer to http://openjena.org/wiki/SDB/Databases_Supported
for additional information. for additional information.
</td> </td>
</tr> </tr>
@ -950,7 +951,7 @@
<tr> <tr>
<td colspan="2"> <td colspan="2">
Specify a driver class name to use a database Specify a driver class name to use a database
other than MySQL. Otherwise, leave this value unchanged. This JAR file other than MySQL. Otherwise, leave this value unchanged. The JAR file
for this driver must be added to the the webapp/lib directory within for this driver must be added to the the webapp/lib directory within
the vitro.core.dir specified above. the vitro.core.dir specified above.
</td> </td>
@ -1026,7 +1027,7 @@
The number of grants and publications is large. The number of grants and publications is large.
</li> </li>
</ul> </ul>
VIVO 1.3 release mitigates this problem by the way of a caching VIVO V1.3 mitigates this problem by the way of a caching
mechanism and hence we can safely set this to be enabled by default. mechanism and hence we can safely set this to be enabled by default.
</td> </td>
</tr> </tr>
@ -1044,11 +1045,11 @@
compare different organizations/people within an organization on compare different organizations/people within an organization on
parameters like number of publications or grants. By default, the app parameters like number of publications or grants. By default, the app
will attempt to make its best guess at the top level organization in 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 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 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 want to identify as the top level organization. It will be used as the
default whenever the temporal graph visualization is rendered without default whenever the temporal graph visualization is rendered without
being passed an explicit org. For example, to use "Ponce School of being passed an explicit org. For example, to use "Ponce School of
Medicine" as the top organization: Medicine" as the top organization:
<br> <br>
<code>visualization.topLevelOrg = <code>visualization.topLevelOrg =
@ -1067,7 +1068,7 @@
<tr> <tr>
<td colspan="2"> <td colspan="2">
An absolute file path, pointing to the root directory of the Harvester utility. An absolute file path, pointing to the root directory of the Harvester utility.
You must include the final slash. You must include the final slash.
Setting a value for harvester.location indicates that the Harvester is installed at Setting a value for harvester.location indicates that the Harvester is installed at
this path. This will enable the Harvester functions in the Ingest Tools page. this path. This will enable the Harvester functions in the Ingest Tools page.
</td> </td>
@ -1108,11 +1109,11 @@
in in
the theme:<pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre> the theme:<pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre>
A sample <code>googleAnalytics.ftl</code> A sample <code>googleAnalytics.ftl</code>
is included in the built-in is included in the built-in
theme. This file serves only as an example, and you must replace the theme. This file serves only as an example, and you must replace the
tracking code shown with your institution's own tracking code. For tracking code shown with your institution's own tracking code. For
additional information about the GATC for the NIH-funded VIVO additional information about the GATC for the NIH-funded VIVO
implementation sites and a copy of your institution's tracking code, 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 see the <a href="https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI">VIVO
Google Google
Analytics Analytics
@ -1142,17 +1143,16 @@
</p> </p>
<p> <p>
6. Start Apache Tomcat and log into VIVO as the root user when the upgrade is 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 completed. Depending on the size of your database, the migration process may
take up to several hours. When it is complete, you will take up to several hours. When it is complete, you will
see a message in the catalina.log file that the server has started. see a message in the catalina.log file that the server has started.<pre>INFO: Server startup in XXXXX ms</pre>
<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". You can check on the
rebuild status by looking at the vivo.all.log in the tomcat logs.
</p> </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". You can check on the
rebuild status by looking at the vivo.all.log in the tomcat logs.
</p>
<h3 id="ontology">IV. Ontology Changes</h3> <h3 id="ontology">IV. Ontology Changes</h3>
<h4 id="verify_ontology_upgrade">i. Verify Ontology upgrade process</h4> <h4 id="verify_ontology_upgrade">i. Verify Ontology upgrade process</h4>
<p> <p>
@ -1167,9 +1167,9 @@
</dt> </dt>
<dd> <dd>
A log of a summary of updates that were made to the knowledge A log of a summary of updates that were made to the knowledge
base and notes about some recommended manual reviews. This file should base and notes about some recommended manual reviews. This file should
end with "Finished knowledge base migration". If this file contains any end with "Finished knowledge base migration". If this file contains any
warnings they should be reviewed with your implementation team warnings they should be reviewed with your implementation team
representative to see whether any corrective action needs to be taken. representative to see whether any corrective action needs to be taken.
</dd> </dd>
</dl> </dl>
@ -1210,11 +1210,11 @@
extensions. extensions.
</p> </p>
<p> <p>
When Apache Tomcat starts up following the upgrade, it will When Apache Tomcat starts up following the upgrade, it will
initiate a process to examine the knowledge base and apply necessary initiate a process to examine the knowledge base and apply necessary
changes. Not all of the modifications that may be required can be changes. Not all of the modifications that may be required can be
automated, so manual review of the knowledge base is recommended after automated, so manual review of the knowledge base is recommended after
the automated upgrade process. The automated process will make only the the automated upgrade process. The automated process will make only the
following types of changes: following types of changes:
</p> </p>
<dl> <dl>
@ -1236,9 +1236,9 @@
All type assertions of a deleted class will be removed. All type assertions of a deleted class will be removed.
<br> <br>
All statements using a deleted property will be changed to use the All statements using a deleted property will be changed to use the
nearest available superproperty. If there is no available superproperty nearest available superproperty. If there is no available superproperty
then the statement will be deleted from the knowledge base. Note that 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 all removed and added data is recorded in the files in the changedData
directory. directory.
</dd> </dd>
</dl> </dl>
@ -1267,11 +1267,26 @@
new default value will be propagated to the knowledge base. new default value will be propagated to the knowledge base.
</dd> </dd>
</dl> </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>
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