Updating from most recent release announcement.
Adding BrianL's note about MySql version.
This commit is contained in:
ejc12
parent
0607ce9128
commit
fad27accef
1 changed files with 186 additions and 197 deletions
383
doc/install.html
383
doc/install.html
|
|
@ -27,95 +27,71 @@
|
|||
</toc>
|
||||
<!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.2</h2>
|
||||
<p>
|
||||
The VIVO 1.2 release incorporates major changes to the entire
|
||||
application - theming and navigation changes that will be immediately
|
||||
evident to any user, and underlying changes to the system architecture
|
||||
that are less visible but address important questions of scalability
|
||||
and extensibility.
|
||||
The VIVO 1.2 release incorporates major changes throughout the
|
||||
application - notably a new templating system to support more flexible
|
||||
display and navigation, plus improvements to address scalability. The
|
||||
release also features two new visualization options: temporal graphing
|
||||
for organizations, and personal visualizations extended to cover grants
|
||||
as well as publications. The VIVO Harvester library has also been
|
||||
significantly improved and expanded in scope for its 1.0 release
|
||||
through the VIVO SourceForge project at
|
||||
<a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
|
||||
</p>
|
||||
<h3>Theming and Navigation</h3>
|
||||
<h4>Templating system for page generation, navigation, and theming</h4>
|
||||
<p>
|
||||
A new installation of VIVO 1.2 will look strikingly different - the
|
||||
User Interface team has designed a new visual theme that incorporates a
|
||||
new navigation and browse structure as well as a much more modular
|
||||
approach to page design. This theme is not only cosmetically different
|
||||
but leverages entirely new page templates developed with the Freemarker
|
||||
system, an open-source library for Java development that enables much
|
||||
cleaner separation of application logic from the actual page design.
|
||||
These changes extend the available configuration options controlling
|
||||
VIVO's appearance and navigation options while also simplifying the
|
||||
process of local customization and branding.
|
||||
A new installation of VIVO 1.2 looks strikingly different, with a
|
||||
new navigation and browse interface as well as a more modular page
|
||||
design that is easier to customize and brand for your local
|
||||
institution. Page displays now support inline navigation to streamline
|
||||
viewing of expanded personal and organizational profiles, as well as
|
||||
improved graphic layout and organization. New browsing controls on the
|
||||
home page and each menu page include interactive visual controls to
|
||||
provide an immediate overview of the size and range of content and
|
||||
quick access down to the individual person, organization, research
|
||||
feature, or event. VIVO's navigation has also been completely
|
||||
overhauled.
|
||||
</p>
|
||||
<h4>Storage model</h4>
|
||||
<p>
|
||||
While server memory capacity has increased significantly in recent
|
||||
years, VIVO's reliance on in-memory caching of RDF data had put limits
|
||||
on the ultimate scalability of VIVO instances and potentially increased
|
||||
the cost of servers required to support VIVO.
|
||||
<br>
|
||||
</p>
|
||||
<p>
|
||||
For existing installations of VIVO, the upgrade will not immediately
|
||||
transition to the new theme, navigation, or page templates. The current
|
||||
default theme and "tabs" (top-level and secondary navigation controls)
|
||||
will be left intact on upgrade and will still function as they do in
|
||||
version 1.1.1, with the caveat that local modifications to the default
|
||||
theme may conflict with internal application changes. We highly
|
||||
recommend that current VIVO installations use the time between release
|
||||
1.2 and the upcoming release of version 1.3 (targeted for June or July
|
||||
2011) to migrate local theme branding and navigation to the new VIVO
|
||||
template. Many legacy features such as the "tab" infrastructure have
|
||||
been deprecated with version 1.2 and will no longer be supported as of
|
||||
version 1.3.
|
||||
With version 1.2, VIVO has been converted to optionally use Jena's
|
||||
SPARQL database (SDB) subsystem. SDB significantly reduces the baseline
|
||||
memory footprint, allowing VIVO installations to scale well beyond what
|
||||
has previously been possible.
|
||||
</p>
|
||||
<h3>Browsing</h3>
|
||||
<h4>New visualizations</h4>
|
||||
<p>
|
||||
In addition to changes in the top-level navigation, VIVO 1.2
|
||||
introduces a number of new browsing controls that will be made more
|
||||
configurable and extensible in version 1.3 but which already offer
|
||||
extensive functionality.
|
||||
VIVO continues to expand visualization options including all-new
|
||||
user-configurable temporal comparisons of publications and grants,
|
||||
grouped by organization or by affiliated person. Visualizations of
|
||||
networks of co-authors are now complemented by visualizations of
|
||||
co-investigators on grants, with a similar interactivity and options
|
||||
for export as images or data.
|
||||
</p>
|
||||
<h4>Ontology</h4>
|
||||
<p>
|
||||
A fresh installation of VIVO 1.2 will feature the new theme and
|
||||
additional browsing options on other top-level navigation pages (Home,
|
||||
People, Research, Organizations, and Events). Primary among the new
|
||||
browsing options will be browsing by <b>type</b>, organized
|
||||
hierarchically with the same upper-level <b>class groups</b>
|
||||
currently
|
||||
visible in search results - people, courses, activities, topics,
|
||||
events, organizations, and publications. Class groups combine the
|
||||
similar types such as people or organizations into groups for browsing
|
||||
and searching, and are locally configurable using the VIVO ontology
|
||||
editor.
|
||||
VIVO 1.2 includes a new ontology module representing research
|
||||
resources including biological specimens, human studies, instruments,
|
||||
organisms, protocols, reagents, and research opportunities. This module
|
||||
is aligned with the top-level ontology classes and properties from the
|
||||
NIH-funded <a href="https://www.eagle-i.org/home/">eagle-i Project</a>.
|
||||
</p>
|
||||
<h3>Associated VIVO releases</h3>
|
||||
<h4>VIVO Harvester</h4>
|
||||
<p>
|
||||
Once a group has been selected, browsing can continue to the very
|
||||
specific, at the level of individual people, organizations, events, or
|
||||
publications via A ... Z listing featuring thumbnail pictures where
|
||||
available. Sites will be able to configure which groups and which types
|
||||
within a group are exposed in search results and for browsing.
|
||||
The Harvester development team is releasing version 1.0 of the VIVO
|
||||
Harvester library, an extensible data ingest and updating framework
|
||||
with sample configurations for loading PubMed publication, grants, and
|
||||
human resources data. The Harvester is available at
|
||||
<a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
|
||||
</p>
|
||||
<h3>Data Storage</h3>
|
||||
<p>
|
||||
Before this release, VIVO has used the Jena (<a href="http://jena.sourceforge.net/" rel="nofollow">http://jena.sourceforge.net</a>)
|
||||
relational
|
||||
database (RDB) subsystem for the storage of RDF data. The
|
||||
performance of this persistence layer has never been fast enough for an
|
||||
interactivity at any significant scale, so VIVO has also maintained a
|
||||
complete copy of data in memory. While server memory capacity has
|
||||
increased significantly in recent years, this requirement has put
|
||||
limits on the ultimate scalability of VIVO instances and also increased
|
||||
the cost of servers required to support VIVO.
|
||||
</p>
|
||||
<p>
|
||||
With version 1.2 VIVO uses the SPARQL database (SDB) subsystem of
|
||||
Jena, specifically designed to support scalable storage and query of
|
||||
RDF datasets while still using standard relational database technology.
|
||||
This transition will significantly reduce the initial memory footprint
|
||||
of a VIVO application, and while the application will still require
|
||||
adequate processor and memory resources to generate pages from so many
|
||||
individual RDF statements, the scalability of VIVO installations is
|
||||
greatly improved.
|
||||
</p>
|
||||
<p>
|
||||
The transition to retrieving all data via SPARQL queries also
|
||||
enables additional features important for tracking data provenance and
|
||||
access to data outside the immediate local VIVO instance. These
|
||||
features will be more fully explored and developed for version 1.3.
|
||||
</p>
|
||||
<!-- Installation process for V1.2 --><h2 id="installation">Installation process for V1.2</h2>
|
||||
<hr><!-- Page break --><!-- Installation process for V1.2 --><h2 id="installation">Installation process for V1.2</h2>
|
||||
<p>
|
||||
This document is a summary of the VIVO installation process. This
|
||||
and other documentation can be found on the <a href="http://vivoweb.org/support">support page</a>
|
||||
|
|
@ -123,9 +99,9 @@
|
|||
</p>
|
||||
<ul>
|
||||
<li>
|
||||
These instructions assume that you are performing a clean
|
||||
install, including emptying an existing database and removing a
|
||||
previous installation from the Tomcat webapps directory. Product
|
||||
These instructions assume that you are performing a clean
|
||||
install, including emptying an existing database and removing a
|
||||
previous installation from the Tomcat webapps directory. Product
|
||||
functionality may not be as expected if you install over an existing
|
||||
installation of an earlier version.
|
||||
</li>
|
||||
|
|
@ -135,8 +111,8 @@
|
|||
</li>
|
||||
</ul>
|
||||
<p>
|
||||
VIVO Developers: If you are working on the VIVO source code from
|
||||
Subversion, the instructions are slightly different. Please consult
|
||||
VIVO Developers: If you are working on the VIVO source code from
|
||||
Subversion, the instructions are slightly different. Please consult
|
||||
developers.txt in this directory.
|
||||
</p>
|
||||
<toc>
|
||||
|
|
@ -151,6 +127,9 @@
|
|||
<li>
|
||||
<a href="#download_code">Download the VIVO Application Source</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="#data_storage">SDB vs RDB</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="#deploy_properties">Specify deployment properties</a>
|
||||
</li>
|
||||
|
|
@ -203,25 +182,31 @@
|
|||
Apache Ant 1.7 or higher, <a href="http://ant.apache.org">http://ant.apache.org</a>
|
||||
</li>
|
||||
<li>
|
||||
MySQL 5.1 or higher, <a href="http://www.mysql.com">http://www.mysql.com</a>
|
||||
MySQL 5.1 or higher*, <a href="http://www.mysql.com">http://www.mysql.com</a>
|
||||
</li>
|
||||
</ul>
|
||||
<p>
|
||||
Be sure to setup the environment variables for <code java_home=""></code>
|
||||
and <code>ANT_HOME</code>
|
||||
and add the executables to your path per
|
||||
your operating system and installation directions from the software
|
||||
and add the executables to your path per
|
||||
your operating system and installation directions from the software
|
||||
support web sites.
|
||||
</p>
|
||||
<p>
|
||||
* Note that VIVO 1.2 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 unsupported
|
||||
versions may result in strange error messages related to table formatting or other
|
||||
unexpected problems.
|
||||
</p>
|
||||
<h3 id="create_database">II. Create an empty MySQL database </h3>
|
||||
<p>
|
||||
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
|
||||
encoding</code>. You will need these values for Step IV when you
|
||||
configure the deployment properties. At the MySQL command line you can
|
||||
encoding</code>. You will need these values for Step IV when you
|
||||
configure the deployment properties. At the MySQL command line you can
|
||||
create the database and user with these commands substituting your
|
||||
values for <code>dbname</code>, <code>username</code>, and <code>password</code>.
|
||||
Most
|
||||
values for <code>dbname</code>, <code>username</code>, and <code>password</code>.
|
||||
Most
|
||||
of
|
||||
the time, the hostname will equal <code>localhost</code>.
|
||||
</p>
|
||||
|
|
@ -244,7 +229,11 @@
|
|||
<br>
|
||||
<a href="http://vivoweb.org/download">http://vivoweb.org/download</a>
|
||||
</p>
|
||||
<h3 id="deploy_properties">IV. Specify deployment properties </h3>
|
||||
<h3 id="data_storage">IV. SDB vs RDB (title)</h3>
|
||||
<p>
|
||||
Content from Brian Lowe coming.
|
||||
</p>
|
||||
<h3 id="deploy_properties">V. Specify deployment properties </h3>
|
||||
<p>
|
||||
At the top level of the unpacked distribution, copy the file <code>example.deploy.properties</code>
|
||||
to a file named simply <code>deploy.properties</code>. This file sets
|
||||
|
|
@ -252,14 +241,14 @@
|
|||
</p>
|
||||
<p>
|
||||
<em>Windows:</em>
|
||||
For those installing on Windows operating
|
||||
system, include the windows drive and use the forward slash "/" and not
|
||||
For those installing on Windows operating
|
||||
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>.
|
||||
</p>
|
||||
<p>
|
||||
<em>External authentication:</em>
|
||||
If you want to use an external
|
||||
authentication system like Shibboleth or CUWebAuth, you will need to
|
||||
If you want to use an external
|
||||
authentication system like Shibboleth or CUWebAuth, you will need to
|
||||
set two additional properties in this file. See the section below
|
||||
entitled <a href="#external_auth">Using an External Authentication
|
||||
System with VIVO</a>.
|
||||
|
|
@ -300,8 +289,8 @@
|
|||
</tr>
|
||||
<tr>
|
||||
<td colspan="2">
|
||||
Directory where Vitro code is located. In most
|
||||
deployments, this is set to ./vitro-core (It is not uncommon for this
|
||||
Directory where Vitro code is located. In most
|
||||
deployments, this is set to ./vitro-core (It is not uncommon for this
|
||||
setting to point elsewhere in development environments).
|
||||
</td>
|
||||
</tr>
|
||||
|
|
@ -341,8 +330,8 @@
|
|||
</tr>
|
||||
<tr>
|
||||
<td colspan="2">
|
||||
Directory where uploaded files will be stored.
|
||||
Be sure this directory exists and is writable by the user that
|
||||
Directory where uploaded files will be stored.
|
||||
Be sure this directory exists and is writable by the user that
|
||||
the Tomcat service is running as.
|
||||
</td>
|
||||
</tr>
|
||||
|
|
@ -356,8 +345,8 @@
|
|||
</tr>
|
||||
<tr>
|
||||
<td colspan="2">
|
||||
Directory where the Lucene search index will be
|
||||
built. Be sure this directory exists and is writable by the user that
|
||||
Directory where the Lucene search index will be
|
||||
built. Be sure this directory exists and is writable by the user that
|
||||
the Tomcat service is running as.
|
||||
</td>
|
||||
</tr>
|
||||
|
|
@ -371,8 +360,8 @@
|
|||
</tr>
|
||||
<tr>
|
||||
<td colspan="2">
|
||||
Specify an SMTP host that the form will use for
|
||||
sending e-mail (Optional). If this is left blank, the contact form will
|
||||
Specify an SMTP host that the form will use for
|
||||
sending e-mail (Optional). If this is left blank, the contact form will
|
||||
be hidden and disabled.
|
||||
</td>
|
||||
</tr>
|
||||
|
|
@ -428,8 +417,8 @@
|
|||
</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
|
||||
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>
|
||||
|
|
@ -444,8 +433,8 @@
|
|||
</tr>
|
||||
<tr>
|
||||
<td colspan="2">
|
||||
Specify the maximum number of active connections
|
||||
in the database connection pool to support the anticipated number of
|
||||
Specify the maximum number of active connections
|
||||
in the database connection pool to support the anticipated number of
|
||||
concurrent page requests. It is not necessary to adjust this value when
|
||||
using the RDB configuration.
|
||||
</td>
|
||||
|
|
@ -460,8 +449,8 @@
|
|||
</tr>
|
||||
<tr>
|
||||
<td colspan="2">
|
||||
Specify the maximum number of database
|
||||
connections that will be allowed to remain idle in the connection pool.
|
||||
Specify the maximum number of database
|
||||
connections that will be allowed to remain idle in the connection pool.
|
||||
Default is 25% of the maximum number of active connections.
|
||||
</td>
|
||||
</tr>
|
||||
|
|
@ -475,9 +464,9 @@
|
|||
</tr>
|
||||
<tr>
|
||||
<td colspan="2">
|
||||
Change the dbtype setting to use a database
|
||||
other than MySQL. Otherwise, leave this value unchanged. Possible
|
||||
values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and
|
||||
Change the dbtype setting to use a database
|
||||
other than MySQL. Otherwise, leave this value unchanged. Possible
|
||||
values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and
|
||||
SQLServer. Refer to http://openjena.org/wiki/SDB/Databases_Supported
|
||||
for additional information.
|
||||
</td>
|
||||
|
|
@ -492,8 +481,8 @@
|
|||
</tr>
|
||||
<tr>
|
||||
<td colspan="2">
|
||||
Specify a driver class name to use a database
|
||||
other than MySQL. Otherwise, leave this value unchanged. This JAR file
|
||||
Specify a driver class name to use a database
|
||||
other than MySQL. Otherwise, leave this value unchanged. This JAR file
|
||||
for this driver must be added to the the webapp/lib directory within
|
||||
the vitro.core.dir specified above.
|
||||
</td>
|
||||
|
|
@ -508,8 +497,8 @@
|
|||
</tr>
|
||||
<tr>
|
||||
<td colspan="2">
|
||||
Change the validation query used to test
|
||||
database connections only if necessary to use a database other than
|
||||
Change the validation query used to test
|
||||
database connections only if necessary to use a database other than
|
||||
MySQL. Otherwise, leave this value unchanged.
|
||||
</td>
|
||||
</tr>
|
||||
|
|
@ -523,8 +512,8 @@
|
|||
</tr>
|
||||
<tr>
|
||||
<td colspan="2">
|
||||
Specify the name of your first admin user for
|
||||
the VIVO application. This user will have an initial temporary password
|
||||
Specify the name of your first admin user for
|
||||
the VIVO application. This user will have an initial temporary password
|
||||
of 'defaultAdmin'. You will be prompted to create a new password on
|
||||
first login.
|
||||
</td>
|
||||
|
|
@ -539,8 +528,8 @@
|
|||
</tr>
|
||||
<tr>
|
||||
<td colspan="2">
|
||||
The URI of a property that can be used to
|
||||
associate an Individual with a user account. When a user logs in with a
|
||||
The URI of a property that can be used to
|
||||
associate an Individual with a user account. When a user logs in with a
|
||||
name that matches the value of this property, the user will be
|
||||
authorized to edit that Individual.
|
||||
</td>
|
||||
|
|
@ -581,7 +570,7 @@
|
|||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<h3 id="deploy">V. Compile and deploy</h3>
|
||||
<h3 id="deploy">VI. Compile and deploy</h3>
|
||||
<p>
|
||||
At the command line, from the top level of the unpacked
|
||||
distribution directory, type:
|
||||
|
|
@ -590,16 +579,16 @@
|
|||
<p>
|
||||
to build VIVO and deploy to Tomcat's webapps directory.
|
||||
</p>
|
||||
<h3 id="tomcat_settings">VI. Set Tomcat JVM parameters and security
|
||||
<h3 id="tomcat_settings">VII. Set Tomcat JVM parameters and security
|
||||
limits</h3>
|
||||
<p>
|
||||
Currently, VIVO copies the contents of your RDF database into
|
||||
memory in order to serve Web requests quickly (the in-memory copy and
|
||||
Currently, VIVO copies the contents of your RDF database into
|
||||
memory in order to serve Web requests quickly (the in-memory copy and
|
||||
the underlying databaseare kept in synch as edits are performed).
|
||||
</p>
|
||||
<p>
|
||||
VIVO will require more memory than that allocated to Tomcat by
|
||||
default. With most installations of Tomcat, the "setenv.sh" or
|
||||
VIVO will require more memory than that allocated to Tomcat by
|
||||
default. With most installations of Tomcat, the "setenv.sh" or
|
||||
"setenv.bat" file in Tomcat's bin directory is a convenient place to
|
||||
set the memory parameters.
|
||||
<br>
|
||||
|
|
@ -608,9 +597,9 @@
|
|||
<pre> export CATALINA_OPTS="-Xms2048m -Xmx1024m -XX:MaxPermSize=128m"<br> </pre>
|
||||
<p>
|
||||
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
|
||||
megabytes is a minimum practical heap size for production installations
|
||||
storing data for large academic institutions, and additional heap space
|
||||
maximum heap of 1024 megabytes, and a PermGen space of 128 megs. 1024
|
||||
megabytes is a minimum practical heap size for production installations
|
||||
storing data for large academic institutions, and additional heap space
|
||||
is preferable. For testing with small sets of data, 256m to 512m should
|
||||
be sufficient.
|
||||
</p>
|
||||
|
|
@ -619,26 +608,26 @@
|
|||
be remedied by increasing the heap parameters and restarting Tomcat.
|
||||
</p>
|
||||
<p>
|
||||
Security limits: VIVO is a multithreaded web application that may
|
||||
require more threads than are permitted under your Linux installation's
|
||||
Security limits: VIVO is a multithreaded web application that may
|
||||
require more threads than are permitted under your Linux installation's
|
||||
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>:
|
||||
</p>
|
||||
<pre> apache hard nproc 400<br> tomcat6 hard nproc 1500 <br> </pre>
|
||||
<h3 id="start_tomcat">VII. Start Tomcat </h3>
|
||||
<h3 id="start_tomcat">VIII. Start Tomcat </h3>
|
||||
<p>
|
||||
Most Tomcat installations can be started by running <code>startup.sh</code>
|
||||
or <code>startup.bat</code>
|
||||
in Tomcat's bin directory. Point your
|
||||
browser to "http://localhost:8080/vivo/" to test the application. If
|
||||
in Tomcat's bin directory. Point your
|
||||
browser to "http://localhost:8080/vivo/" to test the application. If
|
||||
Tomcat does not start up, or the VIVO application is not visible, check
|
||||
the <code>catalina.out</code>
|
||||
file in Tomcat's logs directory.
|
||||
</p>
|
||||
<h3 id="add_rdf">VIII. Log in and add RDF data </h3>
|
||||
<h3 id="add_rdf">IX. Log in and add RDF data </h3>
|
||||
<p>
|
||||
If the startup was successful, you will see a welcome message
|
||||
informing you that you have successfully installed VIVO. Click the "Log
|
||||
If the startup was successful, you will see a welcome message
|
||||
informing you that you have successfully installed VIVO. Click the "Log
|
||||
in" link near the upper right corner. Log in with the <code>initialAdminUser</code>
|
||||
username you set up in Step IV. The initial password for the <code>initialAdminUser</code>
|
||||
account is "defaultAdmin" (without the quotes). On first login, you
|
||||
|
|
@ -647,17 +636,17 @@
|
|||
<p>
|
||||
After verifying your new password, you will be presented with a
|
||||
menu of editing options. Here you can create OWL classes, object
|
||||
properties, data properties, and configure the display of data.
|
||||
Currently, any classes you wish to make visible on your website must be
|
||||
part of a class group, and there a number of visibility and display
|
||||
properties, data properties, and configure the display of data.
|
||||
Currently, any classes you wish to make visible on your website must be
|
||||
part of a class group, and there a number of visibility and display
|
||||
options available for each ontology entity. VIVO comes with a core VIVO
|
||||
ontology, but you may also upload other ontologies from an RDF file.
|
||||
</p>
|
||||
<p>
|
||||
Under the "Advanced Data Tools" click "Add/Remove RDF Data." Note
|
||||
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
|
||||
RDF data you wish to load or upload a file on your local machine.
|
||||
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
|
||||
RDF data you wish to load or upload a file on your local machine.
|
||||
Ensure that the "add RDF" radio button is selected. You will also
|
||||
likely want to check "create classgroups automatically."
|
||||
</p>
|
||||
|
|
@ -669,32 +658,32 @@
|
|||
See more documentation for configuring VIVO, ingesting data, and
|
||||
manually adding data at <a href="http://vivoweb.org/support">http://vivoweb.org/support</a>.
|
||||
</p>
|
||||
<h3 id="contact_email">IX. Set the Contact Email Address (if using
|
||||
<h3 id="contact_email">X. Set the Contact Email Address (if using
|
||||
"Contact Us" form)</h3>
|
||||
<p>
|
||||
If you have configured your application to use the "Contact Us"
|
||||
feature in Step IV (<code>Vitro.smtpHost</code>), you will also need to
|
||||
add an email address to the VIVO application. This is the email
|
||||
feature in Step IV (<code>Vitro.smtpHost</code>), you will also need to
|
||||
add an email address to the VIVO application. This is the email
|
||||
that the contact form submits to. It can be a list server or an
|
||||
individual's email address.
|
||||
</p>
|
||||
<p>
|
||||
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
|
||||
Information" (under "Site Configuration"). In the "Site Information
|
||||
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
|
||||
Information" (under "Site Configuration"). In the "Site Information
|
||||
Editing Form," enter a functional email address in the field "Contact
|
||||
Email Address." and submit the change.
|
||||
</p>
|
||||
<p>
|
||||
If you set the<code>Vitro.smtpHost</code>
|
||||
in Step IV and do NOT
|
||||
provide an email addressin this step, your users will receive a java
|
||||
in Step IV and do NOT
|
||||
provide an email addressin this step, your users will receive a java
|
||||
error in the interface.
|
||||
</p>
|
||||
<h3 id="tomcat_connector">X. Set up Apache Tomcat Connector </h3>
|
||||
<h3 id="tomcat_connector">XI. Set up Apache Tomcat Connector </h3>
|
||||
<p>
|
||||
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.
|
||||
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.
|
||||
8080) and an additional reference to the Tomcat context name (e.g.
|
||||
/vivo).
|
||||
</p>
|
||||
|
|
@ -712,9 +701,9 @@
|
|||
</p>
|
||||
<p>
|
||||
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>)
|
||||
to
|
||||
respond
|
||||
modify the Tomcat's server.xml (located in <code>[tomcat root]/conf/</code>)
|
||||
to
|
||||
respond
|
||||
to requests from Apache via the connector. Look for the
|
||||
<connector> directive and add the following properties:
|
||||
</p>
|
||||
|
|
@ -730,48 +719,48 @@
|
|||
and update as follows:
|
||||
</p>
|
||||
<pre> <Host name="localhost" appBase="webapps"<br> DeployOnStartup="false"<br> unpackWARs="true" autoDeploy="false"<br> xmlValidation="false" xmlNamespaceAware="false"><br> <br> <Alias>example.com</Alias><br> <Context path=""<br> docBase="/usr/local/tomcat/webapps/vivo"<br> reloadable="true"<br> cookies="true" ><br> <Manager pathname="" /><br> <Environment type="java.lang.String" override="false" <br> name="path.configuration" <br> value="deploy.properties"<br> /><br> </Context><br> ...<br> </pre>
|
||||
<h3 id="pellet">XI. Configure Pellet Reasoner </h3>
|
||||
<h3 id="pellet">XII. Configure Pellet Reasoner </h3>
|
||||
<p>
|
||||
<em>Do we need this section still? - elly</em>
|
||||
</p>
|
||||
<p>
|
||||
VIVO uses the Pellet engine to perform reasoning, which runs in the
|
||||
background at startup and also when the knowledge base is edited. VIVO
|
||||
continues serving pages while the reasoner continues working; when the
|
||||
reasoner finishes, the new inferences appear. Inferred statements are
|
||||
background at startup and also when the knowledge base is edited. VIVO
|
||||
continues serving pages while the reasoner continues working; when the
|
||||
reasoner finishes, the new inferences appear. Inferred statements are
|
||||
cached in a database graph so that they are available immediately when
|
||||
VIVO is restarted.
|
||||
</p>
|
||||
<p>
|
||||
By default, Pellet is fed only an incomplete view of your ontology
|
||||
and only certain inferences are materialized. These include rdf:type,
|
||||
rdfs:subClassOf, owl:equivalentClass, and owl:disjointWith. This mode
|
||||
By default, Pellet is fed only an incomplete view of your ontology
|
||||
and only certain inferences are materialized. These include rdf:type,
|
||||
rdfs:subClassOf, owl:equivalentClass, and owl:disjointWith. This mode
|
||||
is typically suitable for ontologies with a lot of instance data. If
|
||||
you would like to keep the default mode, skip to the next step.
|
||||
</p>
|
||||
<p>
|
||||
To enable "complete" OWL inference (materialize all significant
|
||||
entailed statements), open "vitro-core/webapp/config/web.xml" and
|
||||
To enable "complete" OWL inference (materialize all significant
|
||||
entailed statements), open "vitro-core/webapp/config/web.xml" and
|
||||
search for PelletReasonerSetup.
|
||||
</p>
|
||||
<p>
|
||||
Then change the name of the listener class to
|
||||
PelletReasonerSetupComplete. Because "complete" reasoning can be very
|
||||
Then change the name of the listener class to
|
||||
PelletReasonerSetupComplete. Because "complete" reasoning can be very
|
||||
resource intensive, there is also an option to materialize nearly all
|
||||
inferences except owl:sameAs and owl:differentFrom.
|
||||
</p>
|
||||
<p>
|
||||
This is enabled by specifying PelletReasonerSetupPseudocomplete.
|
||||
For ontologies with large numbers of individuals, this mode can offer
|
||||
This is enabled by specifying PelletReasonerSetupPseudocomplete.
|
||||
For ontologies with large numbers of individuals, this mode can offer
|
||||
enormous performance improvements over the "complete" mode.
|
||||
</p>
|
||||
<p>
|
||||
Finally, a class called
|
||||
PelletReasonerSetupPseudocompleteIgnoreDataproperties is provided to
|
||||
Finally, a class called
|
||||
PelletReasonerSetupPseudocompleteIgnoreDataproperties is provided to
|
||||
improve performance on ontologies with large literals where data
|
||||
property entailments are not needed.
|
||||
</p>
|
||||
<h3 id="external_auth">XII. Using an External Authentication System
|
||||
<h3 id="external_auth">XIII. Using an External Authentication System
|
||||
with VIVO </h3>
|
||||
<p>
|
||||
</p>
|
||||
|
|
@ -780,14 +769,14 @@
|
|||
system like Shibboleth or CUWebAuth.
|
||||
</p>
|
||||
<p>
|
||||
VIVO must be accessible only through an Apache HTTP server. The
|
||||
Apache server will be configured to invoke the external authentication
|
||||
VIVO must be accessible only through an Apache HTTP server. The
|
||||
Apache server will be configured to invoke the external authentication
|
||||
system. When the user completes the authentication, the Apache server
|
||||
will pass a network ID to VIVO, to identify the user.
|
||||
</p>
|
||||
<p>
|
||||
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
|
||||
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
|
||||
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.
|
||||
</p>
|
||||
|
|
@ -844,9 +833,9 @@
|
|||
If VIVO has an account for the user, the user will be given the
|
||||
privileges assigned to that account.
|
||||
<p>
|
||||
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
|
||||
data model for a person with a property that matches the User’s network
|
||||
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
|
||||
data model for a person with a property that matches the User’s network
|
||||
ID. You need to tell VIVO what property should be used for matching.
|
||||
Insert a line like this in the deploy.properties file:
|
||||
</p>
|
||||
|
|
@ -854,7 +843,7 @@
|
|||
For example:<pre>selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId</pre>
|
||||
</li>
|
||||
</ul>
|
||||
<h3 id="installation_check">XIII. Was the installation successful? </h3>
|
||||
<h3 id="installation_check">XIV. Was the installation successful? </h3>
|
||||
<p>
|
||||
If you have completed the previous steps, you have good indications
|
||||
that the installation was successful.
|
||||
|
|
@ -878,9 +867,9 @@
|
|||
Click on the "Index" link on the upper right, below the logo.
|
||||
You should see a "locations" section, with links for "Country" and
|
||||
"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
|
||||
periodically to see whether the index will be populated. This may take
|
||||
some time: with VIVO installed on a modest laptop computer, loading the
|
||||
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
|
||||
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
|
||||
time that Tomcat was started.
|
||||
</li>
|
||||
|
|
@ -901,28 +890,28 @@
|
|||
you will be prompted to change the password.
|
||||
</li>
|
||||
<li>
|
||||
After you have successfully logged in, click "site admin" in the
|
||||
upper right corner. In the drop down under "Data Input" select "Faculty
|
||||
After you have successfully logged in, click "site admin" in the
|
||||
upper right corner. In the drop down under "Data Input" select "Faculty
|
||||
Member(core)" and click the "Add individual of this class" button.
|
||||
</li>
|
||||
<li>
|
||||
Enter the name "test individual" under the field "Individual
|
||||
Name," scroll to the bottom, and click "Create New Record." You will be
|
||||
Enter the name "test individual" under the field "Individual
|
||||
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
|
||||
field "URI" it will be used in the next step.
|
||||
</li>
|
||||
<li>
|
||||
Open a new web browser or browser tab to the page <a href="http://marbles.sourceforge.net/">http://marbles.sourceforge.net/</a>.
|
||||
In
|
||||
the
|
||||
Open a new web browser or browser tab to the page <a href="http://marbles.sourceforge.net/">http://marbles.sourceforge.net/</a>.
|
||||
In
|
||||
the
|
||||
pink box on that page enter the URI of the individual you
|
||||
created in the previous step and click "open."
|
||||
</li>
|
||||
<li>
|
||||
In the resulting page search for the URI of the "test
|
||||
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
|
||||
successfully serving linked RDF data. If the URI of the "test
|
||||
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
|
||||
successfully serving linked RDF data. If the URI of the "test
|
||||
individual" is followed by "failed (400)" you are not successfully
|
||||
serving linked data.
|
||||
</li>
|
||||
|
|
@ -932,9 +921,9 @@
|
|||
</p>
|
||||
<ul>
|
||||
<li>
|
||||
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
|
||||
that border Australia, individuals that include Australia, and to
|
||||
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
|
||||
that border Australia, individuals that include Australia, and to
|
||||
Australia itself. To trigger the search index, you can log in as a site
|
||||
administrator and go to "http://your-vivo-url/SearchIndex".
|
||||
</li>
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue