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@ -16,7 +16,7 @@
<div id="wrapper-content" role="main"> <div id="wrapper-content" role="main">
<h1>VIVO Release 1 V1.3 Installation Guide</h1> <h1>VIVO Release 1 V1.3 Installation Guide</h1>
<small> <small>
July 22, 2011 July 29, 2011
</small> </small>
<toc> <toc>
<ul> <ul>
@ -29,96 +29,112 @@
</ul> </ul>
</toc> </toc>
<!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.3</h2> <!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.3</h2>
VIVO Release 1.3 incorporates changes to the search indexing, user <!-- Release Announcement -->VIVO Release 1.3 incorporates changes to the search
accounts, menu management, ontology, and visualizations. indexing, user accounts, menu management, ontology, and visualizations, and begins
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 1.3 will feature notable improvements to the local search, primarily to
of semantic relationships in the search. This will improve recall by improve relevance ranking but also to boost the influence of semantic relationships
including text from related resources (e.g., adding a person’s grant in the search. This will improve recall by including text from related resources
and publication titles to his or her search entry) and by boosting (e.g., adding a person's grant and publication titles to his or her search entry)
overall relevance ranking based on the number and nature of connections and by boosting overall relevance ranking based on the number and nature of
from one individual to others. connections from one individual to others.
<br> </p>
VIVO is now using Apache Solr (http://lucene.apache.org/solr/) in place <p>
of Apache Lucene to improve indexing and faceting of search results. VIVO is now using Apache Solr (http://lucene.apache.org/solr/) in place of
The migration to Solr also aligns the local search with the VIVO Apache Lucene to improve indexing and faceting of search results. The migration
multi-site search site under development for release prior to the 2011 to Solr also aligns the local search with the VIVO multi-site search site under
VIVO Conference. development for release prior to the 2011 VIVO Conference.
<br> </p>
<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 1.3 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.
</p>
<h4>FreeMaker template improvements</h4> <h4>FreeMaker template improvements</h4>
While less directly visible to the public, version 1.3 also includes <p>
additional changes focused directly on supporting open source community While less directly visible to the public, version 1.3 also includes
involvement in extending and customizing VIVO. The development team additional changes focused directly on supporting open source community
began a year ago to transition VIVO’s code base away from Java Server involvement in extending and customizing VIVO. The development team
Pages to the FreeMarker page templating system that much more cleanly began a year ago to transition VIVO&#39;s code base away from Java Server
separates internal application programming logic from page display. Pages to the FreeMarker page templating system that much more cleanly
<br> separates internal application programming logic from page display.
</p>
<h4>Visualization</h4> <h4>Visualization</h4>
The visualization team has implemented a Science Map 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’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 Science Map with one another on the map of science. Wireframes and design
visualization have already been developed; the Science Map 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 visualization 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>
support for certifications and licenses support for certifications and licenses
</li> </li>
<li> <li>
expanded support for intellectual property (patents) (it was expanded support for intellectual property (patents) (it was
there as stub before but didn't allow common things such as assignee there as stub before but didn't allow common things such as assignee
and issuer) and issuer)
</li> </li>
<li> <li>
support for editorial, reviewing and organizing activities support for editorial, reviewing and organizing activities
</li> </li>
<li> <li>
expanded shared geographical instance data vocabulary to include expanded shared geographical instance data vocabulary to include
the 50 U.S. states the 50 U.S. states
</li> </li>
<li> <li>
representing specific types of EducationalTraining: representing specific types of EducationalTraining:
PostdoctoralTraining, Internship, MedicalResidency PostdoctoralTraining, Internship, MedicalResidency
</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 --><!-- Installation process for V1.2 --><h2 id="installation">Installation process for V1.3</h2> <hr><!-- Page break --><!-- Installation process for V1.2 --><h2 id="installation">Installation process for V1.3</h2>
<p> <p>
@ -129,9 +145,9 @@
<ul> <ul>
<li> <li>
These instructions assume that you are performing a clean These instructions assume that you are performing a clean
install, including emptying an existing database, emptying the VIVO install, including emptying an existing database, emptying the VIVO
home directory, and removing a previous installation from the Tomcat home directory, and removing a previous installation from the Tomcat
webapps directory. Product functionality may not be as expected if you webapps directory. Product functionality may not be as expected if you
install over an existing installation of an earlier version. install over an existing installation of an earlier version.
</li> </li>
<li> <li>
@ -140,8 +156,8 @@
</li> </li>
</ul> </ul>
<p> <p>
VIVO Developers: If you are working on the VIVO source code from VIVO Developers: If you are working on the VIVO source code from
Subversion, the instructions are slightly different. Please consult Subversion, the instructions are slightly different. Please consult
developers.txt in this directory. developers.txt in this directory.
</p> </p>
<h3>Where does VIVO live on your computer?</h3> <h3>Where does VIVO live on your computer?</h3>
@ -159,31 +175,31 @@
<h4>VIVO inside Tomcat</h4> <h4>VIVO inside Tomcat</h4>
<p> <p>
When you run the build script to compile and deploy VIVO (see <a href="#deploy">Step VI</a>, below), the files will be deployed to a When you run the build script to compile and deploy VIVO (see <a href="#deploy">Step VI</a>, below), the files will be deployed to a
directory inside Tomcat. This is the actual executing code for VIVO, directory inside Tomcat. This is the actual executing code for VIVO,
but you won’t need to look at it or change it. If you need to change but you won’t need to look at it or change it. If you need to change
VIVO, make the changes in the distribution directory, and run the build VIVO, make the changes in the distribution directory, and run the build
script again. Tell the build script where to find Tomcat by setting <code>tomcat.home</code> script again. Tell the build script where to find Tomcat by setting <code>tomcat.home</code>
in the deploy.properties file (see <a href="#deploy_properties">Step V</a>, in the deploy.properties file (see <a href="#deploy_properties">Step V</a>,
below). below).
</p> </p>
<h4>The VIVO home directory</h4> <h4>The VIVO home directory</h4>
<p> <p>
VIVO will use this area to store some of the data it uses. Uploaded VIVO will use this area to store some of the data it uses. Uploaded
image files are stored here, and the search index is stored here also. image files are stored here, and the search index is stored here also.
You can create this wherever you choose. Tell VIVO where to find the You can create this wherever you choose. Tell VIVO where to find the
home directory by setting <code>vitro.home.directory</code> home directory by setting <code>vitro.home.directory</code>
in the in the
deploy.properties file (see <a href="#deploy_properties">Step V</a>, deploy.properties file (see <a href="#deploy_properties">Step V</a>,
below). You must create this directory before starting VIVO, and you below). You must create this directory before starting VIVO, and you
must ensure that Tomcat has permission to read and write to this must ensure that Tomcat has permission to read and write to this
directory when it runs. directory when it runs.
</p> </p>
<h4>The MySQL database</h4> <h4>The MySQL database</h4>
<p> <p>
Essentially all of the data that you store in VIVO will be given to Essentially all of the data that you store in VIVO will be given to
MySQL for storage. The actual location of this data depends on what MySQL for storage. The actual location of this data depends on what
system you have, and on how you install MySQL (see <a href="#required_software">Step I</a>, below). but you won’t need to system you have, and on how you install MySQL (see <a href="#required_software">Step I</a>, below). but you won’t need to
know the location. You will access the data through VIVO, or know the location. You will access the data through VIVO, or
occasionally through the MySQL client application. occasionally through the MySQL client application.
</p> </p>
<toc> <toc>
@ -228,6 +244,9 @@
<li> <li>
<a href="#installation_check">Was the installation successful?</a> <a href="#installation_check">Was the installation successful?</a>
</li> </li>
<li>
<a href="#termsofuse">Review the VIVO Terms of Use</a>
</li>
</ol> </ol>
</toc> </toc>
<h3 id="required_software">I. Install required software </h3> <h3 id="required_software">I. Install required software </h3>
@ -253,14 +272,14 @@
<p> <p>
Be sure to set up the environment variables for <code java_home="">JAVA_HOME</code> Be sure to set up the environment variables for <code java_home="">JAVA_HOME</code>
and <code>ANT_HOME</code> and <code>ANT_HOME</code>
and add the executables to your path per and add the executables to your path per
your operating system and installation directions from the software your operating system and installation directions from the software
support websites. support websites.
</p> </p>
<p> <p>
* Note that VIVO 1.2 will not run on older versions of MySQL that * Note that VIVO V1.2 or V1.3 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 may have worked with 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 higher. Using unsupported versions may result in strange error messages
related to table formatting or other unexpected problems. related to table formatting or other unexpected problems.
</p> </p>
<p> <p>
@ -270,13 +289,13 @@
<p> <p>
Decide on a database name, username, and password. Log into your Decide on a database name, username, and password. Log into your
MySQL server and create a new database in MySQL that uses <code>UTF-8 MySQL server and create a new database in MySQL that uses <code>UTF-8
encoding</code>. You will need these values for Step IV when you encoding</code>. You will need these values for Step IV when you
configure the deployment properties. At the MySQL command line you can configure the deployment properties. At the MySQL command line you can
create the database and user with these commands substituting your create the database and user with these commands substituting your
values for <code>dbname</code>, <code>username</code>, and <code>password</code>. values for <code>dbname</code>, <code>username</code>, and <code>password</code>.
Most Most
of of
the the
time, the hostname will equal <code>localhost</code>. time, the hostname will equal <code>localhost</code>.
</p> </p>
<pre> CREATE DATABASE dbname CHARACTER SET utf8;<br></pre> <pre> CREATE DATABASE dbname CHARACTER SET utf8;<br></pre>
@ -292,8 +311,8 @@
<br> <br>
</h3> </h3>
<p> <p>
Download the VIVO application source as either <code>rel-1.2.zip</code> Download the VIVO application source as either <code>rel-1.3.zip</code>
or <code>rel-1.2.gz</code> or <code>rel-1.3.gz</code>
file and unpack it on your web server: file and unpack it on your web server:
<br> <br>
<a href="http://vivoweb.org/download">http://vivoweb.org/download</a> <a href="http://vivoweb.org/download">http://vivoweb.org/download</a>
@ -306,15 +325,15 @@
</p> </p>
<p> <p>
<em>Windows:</em> <em>Windows:</em>
For those installing on Windows operating For those installing on Windows operating
system, include the windows drive and use the forward slash "/" and not system, include the windows drive and use the forward slash "/" and not
the back slash "\" in the directory locations, e.g. <code>c:/tomcat</code>. the back slash "\" in the directory locations, e.g. <code>c:/tomcat</code>.
</p> </p>
<p> <p>
<em>External authentication:</em> <em>External authentication:</em>
If you want to use an external If you want to use an external
authentication system like Shibboleth or CUWebAuth, you will need to authentication system like Shibboleth or CUWebAuth, you will need to
set two additional properties in this file. See the section below set two additional properties in this file. See the section below
entitled <a href="#external_auth">Using an External Authentication entitled <a href="#external_auth">Using an External Authentication
System with VIVO</a>. System with VIVO</a>.
</p> </p>
@ -354,8 +373,8 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Directory where Vitro code is located. In most Directory where Vitro code is located. In most
deployments, this is set to ./vitro-core (It is not uncommon for this deployments, this is set to ./vitro-core (It is not uncommon for this
setting to point elsewhere in development environments). setting to point elsewhere in development environments).
</td> </td>
</tr> </tr>
@ -397,8 +416,8 @@
<td colspan="2"> <td colspan="2">
URL of Solr context used in local VIVO search. URL of Solr context used in local VIVO search.
Should consist of:<pre> scheme + servername + port + vivo_webapp_name + "solr"</pre> Should consist of:<pre> scheme + servername + port + vivo_webapp_name + "solr"</pre>
In the standard installation, the Solr context will be on the same 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 server as VIVO, and in the same Tomcat instance. The path will be the
VIVO webapp.name (specified above) + "solr" VIVO webapp.name (specified above) + "solr"
</td> </td>
</tr> </tr>
@ -412,25 +431,24 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Restricts access to the Solr search platform. Restricts access to the Solr search platform.
One or more regular expressions, separated by commas. When a request is 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 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>
@ -444,9 +462,9 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Directory where the VIVO application will store Directory where the VIVO application will 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>
@ -460,9 +478,9 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Specify an SMTP host that the application will Specify an SMTP host that the application will
use for sending e-mail (Optional). If this is left blank, the contact 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 form will be hidden and disabled, and users will not be notified of
changes to their accounts. changes to their accounts.
</td> </td>
</tr> </tr>
@ -478,9 +496,9 @@
<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>
@ -536,25 +554,9 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Specify the Jena triple store technology to use. Specify the maximum number of active connections
SDB is Jena's SPARQL database; this setting allows RDF data to scale in the database connection pool to support the anticipated number of
beyond the limits of the JVM heap. Set to RDB to use the older Jena RDB concurrent page requests. It is not necessary to adjust this value when
store with in-memory caching.
</td>
</tr>
<tr class="odd_row">
<td>
VitroConnection.DataSource.tripleStoreType
</td>
<td>
SDB
</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. using the RDB configuration.
</td> </td>
</tr> </tr>
@ -568,8 +570,8 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Specify the maximum number of database Specify the maximum number of database
connections that will be allowed to remain idle in the connection pool. connections that will be allowed to remain idle in the connection pool.
Default is 25% of the maximum number of active connections. Default is 25% of the maximum number of active connections.
</td> </td>
</tr> </tr>
@ -584,9 +586,9 @@
<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>
@ -600,9 +602,9 @@
</tr> </tr>
<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. This 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>
</tr> </tr>
@ -616,8 +618,8 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Change the validation query used to test Change the validation query used to test
database connections only if necessary to use a database other than database connections only if necessary to use a database other than
MySQL. Otherwise, leave this value unchanged. MySQL. Otherwise, leave this value unchanged.
</td> </td>
</tr> </tr>
@ -636,9 +638,9 @@
temporary password of 'rootPassword'. You will be prompted to create a temporary password of 'rootPassword'. You will be prompted to create a
new password on first login. new password on first login.
<p> <p>
NOTE: The root user account has access to all data and all 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 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 root user. It is best to create a Site Admin account to use for every
day administrative tasks. day administrative tasks.
</p> </p>
</td> </td>
@ -653,9 +655,9 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
The URI of a property that can be used to The URI of a property that can be used to
associate an Individual with a user account. When a user logs in with a 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 name that matches the value of this property, the user will be
authorized to edit that Individual. authorized to edit that Individual.
</td> </td>
</tr> </tr>
@ -667,15 +669,33 @@
http://vivo.mydomain.edu/ns#networkId http://vivo.mydomain.edu/ns#networkId
</td> </td>
</tr> </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> <tr>
<td colspan="2"> <td colspan="2">
The temporal graph visualization can require The temporal graph visualization can require
extensive machine resources. This can have a particularly noticable extensive machine resources. This can have a particularly noticable
impact on memory usage if impact on memory usage if
<ul> <ul>
<li>
VIVO is configured to use Jena SDB,
</li>
<li> <li>
The organization tree is deep, The organization tree is deep,
</li> </li>
@ -683,11 +703,8 @@
The number of grants and publications is large. The number of grants and publications is large.
</li> </li>
</ul> </ul>
The VIVO developers are working to make this visualization more VIVO V1.3 mitigates this problem by the way of a caching
efficient. In the meantime, VIVO release 1.2 guards against this impact mechanism and hence we can safely set this to be enabled by default.
by disabling the temporal graph visualization unless the
"visualization.temporal" flag is set to "enabled". To enable it,
uncomment the line for this setting.
</td> </td>
</tr> </tr>
<tr class="odd_row"> <tr class="odd_row">
@ -706,9 +723,9 @@
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 =
@ -752,14 +769,14 @@
<h3 id="tomcat_settings">VI. Set Tomcat JVM parameters and security <h3 id="tomcat_settings">VI. Set Tomcat JVM parameters and security
limits</h3> limits</h3>
<p> <p>
Currently, VIVO copies the contents of your RDF database into Currently, VIVO copies the contents of your RDF database into
memory in order to serve Web requests quickly (the in-memory copy and memory in order to serve Web requests quickly (the in-memory copy and
the underlying database are kept in synch as edits are performed). the underlying database are kept in synch as edits are performed).
</p> </p>
<p> <p>
VIVO will require more memory than that allocated to Tomcat by VIVO will require more memory than that allocated to Tomcat by
default. With most installations of Tomcat, the "setenv.sh" or default. With most installations of Tomcat, the "setenv.sh" or
"setenv.bat" file in Tomcat's bin directory is a convenient place to "setenv.bat" file in Tomcat's bin directory is a convenient place to
set the memory parameters. <em>If this file does not exist in Tomcat's set the memory parameters. <em>If this file does not exist in Tomcat's
bin directory, you can create it.</em> bin directory, you can create it.</em>
<br> <br>
@ -769,9 +786,9 @@
<p> <p>
This sets Tomcat to allocate an initial heap of 2048 megabytes, a This sets Tomcat to allocate an initial heap of 2048 megabytes, a
maximum heap of 1024 megabytes, and a PermGen space of 128 megs. 1024 maximum heap of 1024 megabytes, and a PermGen space of 128 megs. 1024
megabytes is a minimum practical heap size for production installations megabytes is a minimum practical heap size for production installations
storing data for large academic institutions, and additional heap space storing data for large academic institutions, and additional heap space
is preferable. For testing with small sets of data, 256m to 512m should is preferable. For testing with small sets of data, 256m to 512m should
be sufficient. be sufficient.
</p> </p>
<p> <p>
@ -779,9 +796,9 @@
be remedied by increasing the heap parameters and restarting Tomcat. be remedied by increasing the heap parameters and restarting Tomcat.
</p> </p>
<p> <p>
Security limits: VIVO is a multithreaded web application that may Security limits: VIVO is a multithreaded web application that may
require more threads than are permitted under your Linux installation's require more threads than are permitted under your Linux installation's
default configuration. Ensure that your installation can support the default configuration. Ensure that your installation can support the
required number of threads by making the following edits to <code>/etc/security/limits.conf</code>: required number of threads by making the following edits to <code>/etc/security/limits.conf</code>:
</p> </p>
<pre> apache hard nproc 400<br> tomcat6 hard nproc 1500 <br> </pre> <pre> apache hard nproc 400<br> tomcat6 hard nproc 1500 <br> </pre>
@ -790,39 +807,39 @@
Most Tomcat installations can be started by running <code>startup.sh</code> Most Tomcat installations can be started by running <code>startup.sh</code>
or <code>startup.bat</code> or <code>startup.bat</code>
in Tomcat's bin directory. Point your in Tomcat's bin directory. Point your
browser to "http://localhost:8080/vivo/" to test the application. If browser to "http://localhost:8080/vivo/" to test the application. If
Tomcat does not start up, or the VIVO application is not visible, check Tomcat does not start up, or the VIVO application is not visible, check
the files in Tomcat's logs directory. Error messages are commonly found the files in Tomcat's logs directory. Error messages are commonly found
in <code>catalina.out</code> in <code>catalina.out</code>
or <code>localhost.log</code> or <code>localhost.log</code>
</p> </p>
<h3 id="add_rdf">VIII. Log in and add RDF data </h3> <h3 id="add_rdf">VIII. Log in and add RDF data </h3>
<p> <p>
If the startup was successful, you will see a welcome message If the startup was successful, you will see a welcome message
informing you that you have successfully installed VIVO. Click the "Log informing you that you have successfully installed VIVO. Click the "Log
in" link near the upper right corner. Log in with the <code>rootUser.emailAddress</code> in" link near the upper right corner. Log in with the <code>rootUser.emailAddress</code>
you set up in Step IV. The initial password for the root account is you set up in Step IV. The initial password for the root account is
"rootPassword" (without the quotes). On first login, you will be "rootPassword" (without the quotes). On first login, you will be
prompted to select a new password and verify it a second time. When login is prompted to select a new password and verify it a second time. When login is
complete, the search index is checked and, if it is empty, complete, the search index is checked and, if it is empty,
a full index build will be triggered in the background, in order to ensure a full index build will be triggered in the background, in order to ensure
complete functionality throughout the site. complete functionality throughout the site.
</p> </p>
<p> <p>
After logging in, you will be presented with a After logging in, you will be presented with a
menu of editing options. Here you can create OWL classes, object menu of editing options. Here you can create OWL classes, object
properties, data properties, and configure the display of data. properties, data properties, and configure the display of data.
Currently, any classes you wish to make visible on your website must be Currently, any classes you wish to make visible on your website must be
part of a class group, and there are a number of visibility and display part of a class group, and there are a number of visibility and display
options available for each ontology entity. VIVO comes with a core VIVO options available for each ontology entity. VIVO comes with a core VIVO
ontology, but you may also upload other ontologies from an RDF file. ontology, but you may also upload other ontologies from an RDF file.
</p> </p>
<p> <p>
Under the "Advanced Data Tools" click "Add/Remove RDF Data." Note Under the "Advanced Data Tools" click "Add/Remove RDF Data." Note
that Vitro currently works best with OWL-DL ontologies and has only that Vitro currently works best with OWL-DL ontologies and has only
limited support for pure RDF data. You can enter a URL pointing to the limited support for pure RDF data. You can enter a URL pointing to the
RDF data you wish to load or upload from a file on your local machine. RDF data you wish to load or upload from a file on your local machine.
Ensure that the "add RDF" radio button is selected. You will also Ensure that the "add RDF" radio button is selected. You will also
likely want to check "create classgroups automatically." likely want to check "create classgroups automatically."
</p> </p>
<p> <p>
@ -837,29 +854,29 @@
"Contact Us" form)</h3> "Contact Us" form)</h3>
<p> <p>
If you have configured your application to use the "Contact Us" If you have configured your application to use the "Contact Us"
feature in Step IV (<code>email.smtpHost</code>), you will also need to feature in Step IV (<code>email.smtpHost</code>), you will also need to
add an email address to the VIVO application.&nbsp; This is the email add an email address to the VIVO application.&nbsp; This is the email
to which the contact form will submit. It can be a list server or an to which the contact form will submit. It can be a list server or an
individual's email address. individual's email address.
</p> </p>
<p> <p>
Log in as a system administrator. Navigate to the "Site Admin" Log in as a system administrator. Navigate to the "Site Admin"
table of contents (link in the right side of the header). Go to "Site table of contents (link in the right side of the header). Go to "Site
Information" (under "Site Configuration"). In the "Site Information Information" (under "Site Configuration"). In the "Site Information
Editing Form," enter a functional email address in the field "Contact Editing Form," enter a functional email address in the field "Contact
Email Address" and submit the change. Email Address" and submit the change.
</p> </p>
<p> <p>
If you set the <code>email.smtpHost</code> If you set the <code>email.smtpHost</code>
in Step IV and do NOT in Step IV and do NOT
provide an email address in this step, your users will receive a java provide an email address in this step, your users will receive a java
error in the interface. error in the interface.
</p> </p>
<h3 id="tomcat_connector">X. Set up Apache Tomcat Connector </h3> <h3 id="tomcat_connector">X. Set up Apache Tomcat Connector </h3>
<p> <p>
It is recommended that a Tomcat Connector such as mod_jk be used to It is recommended that a Tomcat Connector such as mod_jk be used to
ensure that the site address does not include the port number (e.g. ensure that the site address does not include the port number (e.g.
8080) and an additional reference to the Tomcat context name (e.g. 8080) and an additional reference to the Tomcat context name (e.g.
/vivo). /vivo).
</p> </p>
<p> <p>
@ -878,9 +895,9 @@
After setting up the mod_jk connector above, you will need to After setting up the mod_jk connector above, you will need to
modify the Tomcat's server.xml (located in <code>[tomcat root]/conf/</code>) modify the Tomcat's server.xml (located in <code>[tomcat root]/conf/</code>)
to to
respond respond
to to
requests from Apache via the connector. Look for the requests from Apache via the connector. Look for the
&lt;connector&gt; directive and add the following properties: &lt;connector&gt; directive and add the following properties:
</p> </p>
<pre> connectionTimeout="20000" maxThreads="320" keepAliveTimeout="20000"&nbsp; <br> </pre> <pre> connectionTimeout="20000" maxThreads="320" keepAliveTimeout="20000"&nbsp; <br> </pre>
@ -904,15 +921,15 @@
system like Shibboleth or CUWebAuth. system like Shibboleth or CUWebAuth.
</p> </p>
<p> <p>
VIVO must be accessible only through an Apache HTTP server. The VIVO must be accessible only through an Apache HTTP server. The
Apache server will be configured to invoke the external authentication Apache server will be configured to invoke the external authentication
system. When the user completes the authentication, the Apache server system. When the user completes the authentication, the Apache server
will pass a network ID to VIVO, to identify the user. will pass a network ID to VIVO, to identify the user.
</p> </p>
<p> <p>
If VIVO has an account for that user, the user will be logged in If VIVO has an account for that user, the user will be logged in
with the privileges of that account. In the absence of an account, VIVO with the privileges of that account. In the absence of an account, VIVO
will try to find a page associated with the user. If such a page is will try to find a page associated with the user. If such a page is
found, the user can log in to edit his own profile information. found, the user can log in to edit his own profile information.
</p> </p>
<h4>Configuring the Apache server</h4> <h4>Configuring the Apache server</h4>
@ -940,9 +957,9 @@
<h5>The name of the HTTP header that will hold the external user's <h5>The name of the HTTP header that will hold the external user's
network ID.</h5> network ID.</h5>
<p> <p>
When a user completes the authentication process, the Apache When a user completes the authentication process, the Apache
server will put the user's network ID into one of the headers of the server will put the user's network ID into one of the headers of the
HTTP request. The instructions from your institution should tell you HTTP request. The instructions from your institution should tell you
which header is used for this purpose. which header is used for this purpose.
</p> </p>
<p> <p>
@ -979,9 +996,9 @@
<p> <p>
In addition, VIVO will try to associate the user with a profile In addition, VIVO will try to associate the user with a profile
page, so the user may edit his own profile data. VIVO will search the page, so the user may edit his own profile data. VIVO will search the
data model for a person with a property that matches the User’s network data model for a person with a property that matches the User’s network
ID (the value of the property must be either a String literal or an ID (the value of the property must be either a String literal or an
untyped literal). You need to tell VIVO what property should be used untyped literal). You need to tell VIVO what property should be used
for matching. Insert a line like this in the deploy.properties file: for matching. Insert a line like this in the deploy.properties file:
</p> </p>
<pre>selfEditing.idMatchingProperty = [the URI of the property]</pre> <pre>selfEditing.idMatchingProperty = [the URI of the property]</pre>
@ -1016,9 +1033,9 @@
You should see a "locations" section, with links for "Country" and You should see a "locations" section, with links for "Country" and
"Geographic Location." The index is built in a background thread, so on "Geographic Location." The index is built in a background thread, so on
your first login, you may see an empty index instead. Refresh the page your first login, you may see an empty index instead. Refresh the page
periodically to see whether the index will be populated. This may take periodically to see whether the index will be populated. This may take
some time: with VIVO installed on a modest laptop computer, loading the some time: with VIVO installed on a modest laptop computer, loading the
ontology files and building the index took more than 5 minutes from the ontology files and building the index took more than 5 minutes from the
time that Tomcat was started. time that Tomcat was started.
</li> </li>
<li> <li>
@ -1038,30 +1055,30 @@
be prompted to change the password. be prompted to change the password.
</li> </li>
<li> <li>
After you have successfully logged in, click "site admin" in the After you have successfully logged in, click "site admin" in the
upper right corner. In the drop down under "Data Input" select "Faculty upper right corner. In the drop down under "Data Input" select "Faculty
Member(core)" and click the "Add individual of this class" button. Member(core)" and click the "Add individual of this class" button.
</li> </li>
<li> <li>
Enter the name "test individual" under the field "Individual Enter the name "test individual" under the field "Individual
Name," scroll to the bottom, and click "Create New Record." You will be Name," scroll to the bottom, and click "Create New Record." You will be
taken to the "Individual Control Panel." Make note of the value of the taken to the "Individual Control Panel." Make note of the value of the
field "URI" - it will be used in the next step. field "URI" - it will be used in the next step.
</li> </li>
<li> <li>
Open a new web browser or browser tab to the page <a href="http://marbles.sourceforge.net/">http://marbles.sourceforge.net/</a>. Open a new web browser or browser tab to the page <a href="http://marbles.sourceforge.net/">http://marbles.sourceforge.net/</a>.
In In
the the
pink pink
box on that page enter the URI of the individual you box on that page enter the URI of the individual you
created in the previous step and click "open." created in the previous step and click "open."
</li> </li>
<li> <li>
In the resulting page search for the URI of the "test In the resulting page search for the URI of the "test
individual." You should find it towards the bottom of the page next to individual." You should find it towards the bottom of the page next to
a red dot followed by "redirect (303)." This indicates that you are a red dot followed by "redirect (303)." This indicates that you are
successfully serving linked RDF data. If the URI of the "test successfully serving linked RDF data. If the URI of the "test
individual" is followed by "failed (400)" you are not successfully individual" is followed by "failed (400)" you are not successfully
serving linked data. serving linked data.
</li> </li>
</ul> </ul>
@ -1071,18 +1088,32 @@
<ul> <ul>
<li> <li>
Type the word "Australia" into the search box, and click on the Type the word "Australia" into the search box, and click on the
Search button.You should see a page of results, with links to countries Search button.You should see a page of results, with links to countries
that border Australia, individuals that include Australia, and to that border Australia, individuals that include Australia, and to
Australia itself. To trigger the search index, you can log in as a site Australia itself. To trigger the search index, you can log in as a site
administrator and go to "http://your-vivo-url/SearchIndex". administrator and go to "http://your-vivo-url/SearchIndex".
</li> </li>
</ul> </ul>
<h3 id="termsofuse">XIII. 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> </div>
<!-- #wrapper-content --> <!-- #wrapper-content -->
<div id="footer" role="contentinfo"> <div id="footer" role="contentinfo">
<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
</small> </small>
| Powered | Powered
by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a> by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a>

225
doc/upgrade-1.3.html
View file

@ -14,7 +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 28, 2011 - Upgrading from Release 1 V1.2 to Release 1 V1.3 July 29, 2011 - Upgrading from Release 1 V1.2 to Release 1 V1.3
</small> </small>
<toc> <toc>
<ul> <ul>
@ -61,30 +61,30 @@
</p> </p>
<h4>Authorization</h4> <h4>Authorization</h4>
<p> <p>
Release V1.3 provides an entirely new model of authorization within the 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.
</p> </p>
<h4>Menu management</h4> <h4>Menu management</h4>
<p> <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.
</p> </p>
<h4>FreeMarker template improvements</h4> <h4>FreeMarker template improvements</h4>
<p> <p>
While less directly visible to the public, V1.3 also includes 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.
</p> </p>
<h4>Visualization</h4> <h4>Visualization</h4>
@ -93,12 +93,12 @@
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.
</p> </p>
<p> <p>
@ -227,10 +227,10 @@
</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>
@ -238,10 +238,10 @@
</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.
@ -269,20 +269,20 @@
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 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>.
@ -298,12 +298,12 @@
</p> </p>
<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>
@ -364,21 +364,21 @@
<toc> <toc>
<ul> <ul>
<li> <li>
The file used to register list views has changed to a directory where new The file used to register list views has changed to a directory where new<code>.rdf</code>
<code>.rdf</code> or <code>.n3</code> files can be placed: or <code>.n3</code>
<code>/vivo/productMods/WEB-INF/ontologies/app/loadedAtStartup</code>. The rdf required files can be placed: <code>/vivo/productMods/WEB-INF/ontologies/app/loadedAtStartup</code>. The rdf required
to register a new view has not changed. to register a new view has not changed.
</li> </li>
<li> <li>
<code>&lt;query-base&gt;</code> and <code>&lt;query-collated&gt;</code> <code>&lt;query-base&gt;</code>
and <code>&lt;query-collated&gt;</code>
have been replaced with a single query <code>&lt;query-select&gt;</code> have been replaced with a single query <code>&lt;query-select&gt;</code>
that contains tags for fragments to be used only in the collated that contains tags for fragments to be used only in the collated
version of the query. version of the query.
</li> </li>
</ul> </ul>
<p> <p>
These and other changes are documented in greater detail in These and other changes are documented in greater detail in<code style="whitespace:nowrap;">/vitro/doc/list_view_configuration_guidelines.txt</code>.
<code style="whitespace:nowrap;">/vitro/doc/list_view_configuration_guidelines.txt</code>.
</p> </p>
</toc> </toc>
<h4 id="authorization">v. Authorization</h4> <h4 id="authorization">v. Authorization</h4>
@ -507,23 +507,23 @@
<dl style="margin-left: 40px;"> <dl style="margin-left: 40px;">
<dd> <dd>
<p> <p>
If you are upgrading to VIVO V1.3 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 V1.3 part of your migration to V1.3
</p> </p>
</dd> </dd>
@ -552,10 +552,10 @@
<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>
@ -625,12 +625,12 @@
<div style="margin-left: 40px;"> <div style="margin-left: 40px;">
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;">
@ -641,11 +641,11 @@
<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 account. 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 here which ins not visible to other accounts. shown here which ins not visible to other accounts.
</p> </p>
@ -665,10 +665,10 @@
</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>
@ -835,10 +835,10 @@
<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>
@ -893,23 +893,6 @@
password password
</td> </td>
</tr> </tr>
<tr>
<td colspan="2">
Specify the Jena triple store technology to
use.
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
store with in-memory caching.
</td>
</tr>
<tr class="odd_row">
<td>
VitroConnection.DataSource.tripleStoreType
</td>
<td>
SDB
</td>
</tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Specify the maximum number of active Specify the maximum number of active
@ -1022,15 +1005,33 @@
http://vivo.mydomain.edu/ns#networkId http://vivo.mydomain.edu/ns#networkId
</td> </td>
</tr> </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> <tr>
<td colspan="2"> <td colspan="2">
The temporal graph visualization can require The temporal graph visualization can require
extensive machine resources. This can have a particularly noticable extensive machine resources. This can have a particularly noticable
impact on memory usage if impact on memory usage if
<ul> <ul>
<li>
VIVO is configured to use Jena SDB,
</li>
<li> <li>
The organization tree is deep, The organization tree is deep,
</li> </li>
@ -1055,12 +1056,12 @@
The temporal graph visualization is used to The temporal graph visualization is used to
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 =
@ -1078,7 +1079,7 @@
</tr> </tr>
<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.
@ -1121,10 +1122,10 @@
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
@ -1222,10 +1223,10 @@
</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>