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@ -14,8 +14,7 @@
<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 July 22, 2011 - Upgrading from Release 1 v1.2 to Release 1 v1.3
v1.3
</small> </small>
<toc> <toc>
<ul> <ul>
@ -43,12 +42,99 @@
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>
<p> V<!-- Release Announcement -->IVO Release 1.3 incorporates changes to
https://confluence.cornell.edu/x/3B4DCQ - get content from the wiki the search indexing, user
page before final release. accounts, menu management, ontology, and visualizations.
<br> <br>
</p> <h4>Search</h4>
<!-- Release Announcement --><hr><!-- Page break --><!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.3</h2> VIVO 1.3 will feature notable improvements to the local search,
primarily to improve relevance ranking but also to boost the influence
of semantic relationships in the search. This will improve recall by
including text from related resources (e.g., adding a person’s grant
and publication titles to his or her search entry) and by boosting
overall relevance ranking based on the number and nature of connections
from one individual to others.
<br>
VIVO is now using Apache Solr (http://lucene.apache.org/solr/) in place
of Apache Lucene to improve indexing and faceting of search results.
The migration to Solr also aligns the local search with the VIVO
multi-site search site under development for release prior to the 2011
VIVO Conference.
<br>
<h4>Authorization</h4>
Release 1.3 provides an entirely new model of authorization within the
VIVO application to allow more granular control over system
configuration and editing. The first phase of the new user account
interface is included in V1.3. This interface provides a user search, a
root acount, and password reset functionality where the password gets
emailed to the user. The next phase will provide the ability to create
new roles.
<br>
<h4>Menu management</h4>
The menus across the top of the site (Home, People, Organizations,
Research, Events) can now be managed in a web form instead of editing
an RDF file. In addition to making site management much easier,
form-based editing also allows more control over what classes of data
are displayed and provides a mechanism to limit certain menu pages to
content identified as internal to the institution.
<br>
<h4>FreeMaker template improvements</h4>
While less directly visible to the public, version 1.3 also includes
additional changes focused directly on supporting open source community
involvement in extending and customizing VIVO. The development team
began a year ago to transition VIVO’s code base away from Java Server
Pages to the FreeMarker page templating system that much more cleanly
separates internal application programming logic from page display.
<br>
<h4>Visualization</h4>
The visualization team has implemented a Science Map visualization,
which allows users to visually explore the scientific strengths of a
university, school, department, or person in the VIVO instance. Users
will be able to see where an organization or person’s interests lay
across 13 major scientific disciplines or 554 sub-disciplines, and will
be able to see how these disciplines and sub-disciplines interrelate
with one another on the map of science. Wireframes and design
documentation for upcoming enhanced versions of the Science Map
visualization have already been developed; the Science Map
visualization will most likely be in the form of a PDF that a user can
download.
<br>
Several visualization also now provide a caching feature that improves
performance after the initial processing.
<br>
<h4>QR Codes</h4>
Pages for people in VIVO have the option of displaying QR codes.
<br>
<h4>Ontology changes</h4>
<ul>
<li>
support for certifications and licenses
</li>
<li>
expanded support for intellectual property (patents) (it was
there as stub before but didn't allow common things such as assignee
and issuer)
</li>
<li>
support for editorial, reviewing and organizing activities
</li>
<li>
expanded shared geographical instance data vocabulary to include
the 50 U.S. states
</li>
<li>
representing specific types of EducationalTraining:
PostdoctoralTraining, Internship, MedicalResidency
</li>
</ul>
<h4>Linked open data</h4>
Responses to linked data requests have been enhanced to include
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
RDF via a single web request.
<br>
<br>
<hr><!-- Page break --><!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.3</h2>
<toc> <toc>
<ol class="roman1"> <ol class="roman1">
<li> <li>
@ -92,14 +178,10 @@
</li> </li>
<li> <li>
<a href="#root_account">Each VIVO installation will have a <a href="#root_account">Each VIVO installation will have a
“root” account</a> 'root' account</a>
</li> </li>
</ol> </ol>
</li> </li>
<li>
<a href="#setup_sdb">Set Up SDB Store in the Background
(Optional)</a>
</li>
</ol> </ol>
</toc> </toc>
<h3 id="preparation">I. Before Performing the Upgrade</h3> <h3 id="preparation">I. Before Performing the Upgrade</h3>
@ -123,8 +205,8 @@
</p> </p>
<ul> <ul>
<li> <li>
If you are still in RDB mode, it is required that you If you are still in RDB mode, it is required that you move your
move your triple store to SDB while still at V1.2 (see <a href="ejc12_upgrade-1.3.html#triple_store">Triple Store</a> triple store to SDB while still at V1.2 (see <a href="ejc12_upgrade-1.3.html#triple_store">Triple Store</a>
info info
below).&nbsp; below).&nbsp;
<br> <br>
@ -144,7 +226,8 @@
First-time login of the administrator account after the upgrade First-time login of the administrator account after the 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. installation. With V1.3 there is also a new root user. Please see the
section on <a href="#authorization">Authorization changes</a> for more information.
</li> </li>
<li> <li>
The first time Apache Tomcat starts up after the upgrade, it The first time Apache Tomcat starts up after the upgrade, it
@ -158,15 +241,15 @@
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 were available in VIVO 1.2 and 1.2.1.&nbsp; It is required that you
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>
SDB mode caches only a fraction of the RDF data in memory. Most SDB mode caches only a fraction of the RDF data in memory. Most
queries are issued directly against the underlying database. This queries are issued directly against the underlying database. This
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 make take slightly longer There is a tradeoff in response time: pages may take slightly longer
to load in SDB mode, and performance will depend on the configuration to 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.
@ -176,15 +259,14 @@
</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 complete if the installation contains a large amount of RDF data
installation contains a large amount of RDF data (roughly a million (roughly a million triples or more).&nbsp; You can start the conversion
triples or more).&nbsp; You can start the conversion process in the process in the background while the RDB system is running. This will
background reduce the delay in initial startup after the application is redeployed
while the RDB system is running. This will reduce the delay in initial with deploy.properties set for SDB. <span style="font-weight: bold;">Note
startup after the application is redeployed with deploy.properties set that
for SDB. <span style="font-weight: bold;">Note that it is important it is important not to edit any data anywhere in the application
not to edit any data anywhere in the while this background conversion is running</span>.
application 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
@ -215,14 +297,14 @@
2. Create a new deploy.properties using the same values as in your 2. Create a new deploy.properties using the same values as in 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, vitro.home.directory, email.smptHost, email.replyTo,
email.smptHost, email.replyTo, rootUser.emailAddress) rootUser.emailAddress)
<br> <br>
</p> </p>
<p> <p>
<!-- deploy.properties table from install.html --> <!-- deploy.properties table from install.html -->
</p> </p>
<table> <table border='1' bordercolor="#CCCCCC" cellspacing="5">
<tbody> <tbody>
<tr> <tr>
<th> <th>
@ -650,9 +732,7 @@
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 wiki page</a>.
wiki
page</a>.
</li> </li>
<li> <li>
If you had used the <code>vivo/contrib/FLShibboleth</code> If you had used the <code>vivo/contrib/FLShibboleth</code>
@ -671,7 +751,7 @@
that modification. that modification.
</p> </p>
<p> <p>
5. Stop Apache Tomcat and run ant by typing: <code>ant all</code> 5. Stop Apache Tomcat and from your VIVO source directory, run ant by typing: <code>ant all</code>
</p> </p>
<p> <p>
6. Start Apache Tomcat and log in to VIVO. 6. Start Apache Tomcat and log in to VIVO.
@ -790,14 +870,14 @@
<ul> <ul>
<li> <li>
<p> <p>
The <code>${stylesheets}</code>, <code>${scripts}</code>, and <code>${headScripts}</code> The <code>${stylesheets}</code>, <code>${scripts}</code>, and<code>${headScripts}</code>
<code>add()</code> <code>add()</code>
methods now methods now take
take the full tag as an argument. This will require a change to all the full tag as an argument. This will require a change to all calls to
calls to these methods in the templates. This change allows for these methods in the templates. This change allows for specification of
specification of attributes such as <code>media</code> attributes such as <code>media</code>
directly directly in the tag. For
in the tag. For example: example:
</p> </p>
<blockquote> <blockquote>
1.2: <code>${stylesheets.add("/css/individual/individual.css")}</code> 1.2: <code>${stylesheets.add("/css/individual/individual.css")}</code>
@ -808,36 +888,31 @@
<p> <p>
Note the inclusion of <code>${urls.base}</code> Note the inclusion of <code>${urls.base}</code>
in the 1.3 in the 1.3
example. example. The <code>add()</code>
The <code>add()</code> method no longer prefixes the context
method no longer prefixes the context path to path to the url, so the full url must be specified in the tag.
the url, so the full
url must be specified in the tag.
</p> </p>
</li> </li>
<li> <li>
The <code>addFromTheme()</code> The <code>addFromTheme()</code>
methods of the <code>${stylesheets}</code>,<code>${scripts}</code>, and<code>${headScripts}</code> methods of the <code>${stylesheets}</code>,<code>${scripts}</code>,
objects have been deleted. Substitute and<code>${headScripts}</code>
as shown in the objects have been deleted. Substitute as
preceding example. shown in the preceding example.
</li> </li>
<li> <li>
<code>propertyGroups.getPropertyAndRemoveFromList()</code> <code>propertyGroups.getPropertyAndRemoveFromList()</code>
in the in
individual templates has been deprecated. The replacement method is <code>propertyGroups.pullProperty()</code>. the individual templates has been deprecated. The replacement method is<code>propertyGroups.pullProperty()</code>. There is no change in
There is no change in functionality. functionality.
</li> </li>
</ul> </ul>
<h3 id="listview">VI. List view changes</h3> <h3 id="listview">VI. List view changes</h3>
<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>
have been replaced have been replaced with a single query <code>&lt;query-select&gt;</code>
with a single query <code>&lt;query-select&gt;</code> that contains tags for fragments to be used only in the collated
that contains version of the query. This and other changes are documented in <code>/vitro/doc/list_view_configuration_guidelines.txt</code>.<h3 id="authorization">VII. Authorization changes</h3>
tags for
fragments to be used only in the collated version of the query. This
and other changes are documented in <code>/vitro/doc/list_view_configuration_guidelines.txt</code>.<h3 id="authorization">VII. Authorization changes</h3>
<p> <p>
In release 1.3, the VIVO authorization system has some extensive In release 1.3, the VIVO authorization system has some extensive
changes. In summary, these are: changes. In summary, these are:
@ -879,7 +954,7 @@
<p> <p>
Prior to release 1.3, each user account was identified by a Prior to release 1.3, each user account was identified by a
Username field. This field was labeled as “E-mail address” on some Username field. This field was labeled as “E-mail address” on some
pages in VIVO, but so mail was ever sent. In release 1.3, this has pages in VIVO, but no mail was ever sent. In release 1.3, 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>
@ -890,7 +965,7 @@
<dd> <dd>
<p> <p>
Prior to release 1.3, the Username field (also referred to as Prior to release 1.3, 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>
@ -914,7 +989,8 @@
</p> </p>
<ul> <ul>
<li> <li>
EmailAddress is used when logging in (along with a password). EmailAddress is used when logging in (along with a
password).
</li> </li>
<li> <li>
EmailAddress is used to send notifications to the user about EmailAddress is used to send notifications to the user about
@ -956,7 +1032,8 @@
<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 should plan for this as part of your migration to release 1.3 You
should plan for this as part of your migration to release 1.3
</p> </p>
</dd> </dd>
</dl> </dl>
@ -1003,9 +1080,9 @@
<dd> <dd>
<p> <p>
The e-mail notification relies on two configuration properties:<code>email.smtpHost</code> The e-mail notification relies on two configuration properties:<code>email.smtpHost</code>
and <code>email.replyTo</code>. If and <code>email.replyTo</code>. If either of these properties is
either of these properties is missing or empty, VIVO will not attempt missing or empty, VIVO will not attempt to send e-mail notifications to
to send e-mail notifications to users. users.
</p> </p>
<p> <p>
This can be useful for small or experimental installations of This can be useful for small or experimental installations of
@ -1019,7 +1096,7 @@
</p> </p>
</dd> </dd>
</dl> </dl>
<h4 id="root_account">iii. Each VIVO installation will have a “root” <h4 id="root_account">iii. Each VIVO installation will have a 'root'
account.</h4> account.</h4>
<dl> <dl>
<dd> <dd>
@ -1034,7 +1111,8 @@
</p> </p>
<pre>rootUser.emailAddress = vivo_root@mydomain.edu</pre> <pre>rootUser.emailAddress = vivo_root@mydomain.edu</pre>
The password for this account is automatically set to <code>rootPassword</code>, The password for this account is automatically set to <code>rootPassword</code>,
but you will be required to change the password the first time you log but
you will be required to change the password the first time you log
in. in.
<blockquote> <blockquote>
<strong>Note:</strong> <strong>Note:</strong>