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doc/upgrade-1.3.html
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@ -1,4 +1,4 @@
<!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>
Release V1.3 provides an entirely new model of authorization within the
VIVO application to allow more granular control over system VIVO application to allow more granular control over system
configuration and editing. The first phase of the new user account configuration and editing. The first phase of the new user account
interface is included in V1.3. This interface provides a user search, a interface is included in V1.3. This interface provides a user search, a
root acount, and password reset functionality where the password gets root acount, and password reset functionality where the password gets
emailed to the user. The next phase will provide the ability to create emailed to the user. The next phase will provide the ability to create
new roles. new roles.
<br> </p>
<h4>Menu management</h4> <h4>Menu management</h4>
<p>
The menus across the top of the site (Home, People, Organizations, The menus across the top of the site (Home, People, Organizations,
Research, Events) can now be managed in a web form instead of editing Research, Events) can now be managed in a web form instead of editing
an RDF file. In addition to making site management much easier, an RDF file. In addition to making site management much easier,
form-based editing also allows more control over what classes of data form-based editing also allows more control over what classes of data
are displayed and provides a mechanism to limit certain menu pages to are displayed and provides a mechanism to limit certain menu pages to
content identified as internal to the institution. content identified as internal to the institution.
<br> </p>
<h4>FreeMaker template improvements</h4> <h4>FreeMarker template improvements</h4>
While less directly visible to the public, version 1.3 also includes <p>
While less directly visible to the public, V1.3 also includes
additional changes focused directly on supporting open source community additional changes focused directly on supporting open source community
involvement in extending and customizing VIVO. The development team involvement in extending and customizing VIVO. The development team
began a year ago to transition VIVO&#39;s code base away from Java Server began a year ago to transition VIVO&#39;s code base away from Java Server
Pages to the FreeMarker page templating system that much more cleanly Pages to the FreeMarker page templating system that much more cleanly
separates internal application programming logic from page display. separates internal application programming logic from page display.
<br> </p>
<h4>Visualization</h4> <h4>Visualization</h4>
<p>
The visualization team has implemented a Map of Science visualization, The visualization team has implemented a Map of Science visualization,
which allows users to visually explore the scientific strengths of a which allows users to visually explore the scientific strengths of a
university, school, department, or person in the VIVO instance. Users university, school, department, or person in the VIVO instance. Users
will be able to see where an organization or person&#39;s interests lay will be able to see where an organization or person&#39;s interests lay
across 13 major scientific disciplines or 554 sub-disciplines, and will across 13 major scientific disciplines or 554 sub-disciplines, and will
be able to see how these disciplines and sub-disciplines interrelate be able to see how these disciplines and sub-disciplines interrelate
with one another on the map of science. Wireframes and design with one another on the Map of Science. Wireframes and design
documentation for upcoming enhanced versions of the Map of Science documentation for upcoming enhanced versions of the Map of Science
visualization have already been developed; the Map of Science visualization have already been developed; the Map of Science
visualization will most likely be in the form of a PDF that a user can visualization will most likely be in the form of a PDF that a user can
download. download.
<br> </p>
Several visualization also now provide a caching feature that improves <p>
Several visualizations also now provide a caching feature that improves
performance after the initial processing. performance after the initial processing.
<br> </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>
<p>
Responses to linked data requests have been enhanced to include Responses to linked data requests have been enhanced to include
additional context about any individual, in working toward a goal of additional context about any individual, in working toward a goal of
being able to provide all the data in a person's profile available as being able to provide all the data in a person's profile available as
RDF via a single web request. RDF via a single web request.
<br> </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>
@ -236,9 +253,8 @@
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>
@ -273,7 +289,7 @@
</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>
@ -292,7 +308,7 @@
</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
@ -303,16 +319,14 @@
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
full tag as an argument.
This will require a change to all calls to these methods in the 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:
@ -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>
@ -385,32 +398,27 @@
<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>
@ -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>
@ -494,7 +496,7 @@
<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
@ -511,7 +513,7 @@
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>
@ -565,7 +567,7 @@
</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>
@ -573,7 +575,7 @@
<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.
@ -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;">
@ -622,23 +624,23 @@
</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.
@ -762,8 +764,7 @@
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
@ -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>
@ -1144,8 +1145,7 @@
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>
<p> <p>
7. As root or an administrator, request a rebuild of the Solr search index: 7. As root or an administrator, request a rebuild of the Solr search index:
@ -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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<p class="copyright"> <p class="copyright">
<small> <small>
©2011 All Rights Reserved | <a class="terms" href="/termsOfUse">Terms of Use</a> ©2011 All Rights Reserved
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