Merging from maint 1.3 (3420) for upgrade (3409) and install (3361).
This commit is contained in:
ejc12
parent
89db251ea4
commit
e73af0d9a4
2 changed files with 397 additions and 365 deletions
537
doc/install.html
537
doc/install.html
|
|
@ -16,7 +16,7 @@
|
|||
<div id="wrapper-content" role="main">
|
||||
<h1>VIVO Release 1 V1.3 Installation Guide</h1>
|
||||
<small>
|
||||
July 22, 2011
|
||||
July 29, 2011
|
||||
</small>
|
||||
<toc>
|
||||
<ul>
|
||||
|
|
@ -29,96 +29,112 @@
|
|||
</ul>
|
||||
</toc>
|
||||
<!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.3</h2>
|
||||
VIVO Release 1.3 incorporates changes to the search indexing, user
|
||||
accounts, menu management, ontology, and visualizations.
|
||||
<!-- Release Announcement -->VIVO Release 1.3 incorporates changes to the search
|
||||
indexing, user accounts, menu management, ontology, and visualizations, and begins
|
||||
integration of VIVO Harvester functions with VIVO's own ingest tools.
|
||||
<br>
|
||||
<h4>Search</h4>
|
||||
VIVO 1.3 will feature notable improvements to the local search,
|
||||
primarily to improve relevance ranking but also to boost the influence
|
||||
of semantic relationships in the search. This will improve recall by
|
||||
including text from related resources (e.g., adding a person’s grant
|
||||
and publication titles to his or her search entry) and by boosting
|
||||
overall relevance ranking based on the number and nature of connections
|
||||
from one individual to others.
|
||||
<br>
|
||||
VIVO is now using Apache Solr (http://lucene.apache.org/solr/) in place
|
||||
of Apache Lucene to improve indexing and faceting of search results.
|
||||
The migration to Solr also aligns the local search with the VIVO
|
||||
multi-site search site under development for release prior to the 2011
|
||||
VIVO Conference.
|
||||
<br>
|
||||
<p>
|
||||
VIVO 1.3 will feature notable improvements to the local search, primarily to
|
||||
improve relevance ranking but also to boost the influence of semantic relationships
|
||||
in the search. This will improve recall by including text from related resources
|
||||
(e.g., adding a person's grant and publication titles to his or her search entry)
|
||||
and by boosting overall relevance ranking based on the number and nature of
|
||||
connections from one individual to others.
|
||||
</p>
|
||||
<p>
|
||||
VIVO is now using Apache Solr (http://lucene.apache.org/solr/) in place of
|
||||
Apache Lucene to improve indexing and faceting of search results. The migration
|
||||
to Solr also aligns the local search with the VIVO multi-site search site under
|
||||
development for release prior to the 2011 VIVO Conference.
|
||||
</p>
|
||||
<h4>Authorization</h4>
|
||||
Release 1.3 provides an entirely new model of authorization within the
|
||||
VIVO application to allow more granular control over system
|
||||
configuration and editing. The first phase of the new user account
|
||||
interface is included in V1.3. This interface provides a user search, a
|
||||
root acount, and password reset functionality where the password gets
|
||||
emailed to the user. The next phase will provide the ability to create
|
||||
new roles.
|
||||
<br>
|
||||
<p>
|
||||
Release 1.3 provides an entirely new model of authorization within the
|
||||
VIVO application to allow more granular control over system
|
||||
configuration and editing. The first phase of the new user account
|
||||
interface is included in V1.3. This interface provides a user search, a
|
||||
root acount, and password reset functionality where the password gets
|
||||
emailed to the user. The next phase will provide the ability to create
|
||||
new roles.
|
||||
</p>
|
||||
<h4>Menu management</h4>
|
||||
The menus across the top of the site (Home, People, Organizations,
|
||||
Research, Events) can now be managed in a web form instead of editing
|
||||
an RDF file. In addition to making site management much easier,
|
||||
form-based editing also allows more control over what classes of data
|
||||
are displayed and provides a mechanism to limit certain menu pages to
|
||||
content identified as internal to the institution.
|
||||
<br>
|
||||
<p>
|
||||
The menus across the top of the site (Home, People, Organizations,
|
||||
Research, Events) can now be managed in a web form instead of editing
|
||||
an RDF file. In addition to making site management much easier,
|
||||
form-based editing also allows more control over what classes of data
|
||||
are displayed and provides a mechanism to limit certain menu pages to
|
||||
content identified as internal to the institution.
|
||||
</p>
|
||||
<h4>FreeMaker template improvements</h4>
|
||||
While less directly visible to the public, version 1.3 also includes
|
||||
additional changes focused directly on supporting open source community
|
||||
involvement in extending and customizing VIVO. The development team
|
||||
began a year ago to transition VIVO’s code base away from Java Server
|
||||
Pages to the FreeMarker page templating system that much more cleanly
|
||||
separates internal application programming logic from page display.
|
||||
<br>
|
||||
<p>
|
||||
While less directly visible to the public, version 1.3 also includes
|
||||
additional changes focused directly on supporting open source community
|
||||
involvement in extending and customizing VIVO. The development team
|
||||
began a year ago to transition VIVO's code base away from Java Server
|
||||
Pages to the FreeMarker page templating system that much more cleanly
|
||||
separates internal application programming logic from page display.
|
||||
</p>
|
||||
<h4>Visualization</h4>
|
||||
The visualization team has implemented a Science Map visualization,
|
||||
which allows users to visually explore the scientific strengths of a
|
||||
university, school, department, or person in the VIVO instance. Users
|
||||
will be able to see where an organization or person’s interests lay
|
||||
across 13 major scientific disciplines or 554 sub-disciplines, and will
|
||||
be able to see how these disciplines and sub-disciplines interrelate
|
||||
with one another on the map of science. Wireframes and design
|
||||
documentation for upcoming enhanced versions of the Science Map
|
||||
visualization have already been developed; the Science Map
|
||||
visualization will most likely be in the form of a PDF that a user can
|
||||
download.
|
||||
<br>
|
||||
Several visualization also now provide a caching feature that improves
|
||||
performance after the initial processing.
|
||||
<br>
|
||||
<p>
|
||||
The visualization team has implemented a Map of Science visualization,
|
||||
which allows users to visually explore the scientific strengths of a
|
||||
university, school, department, or person in the VIVO instance. Users
|
||||
will be able to see where an organization or person's interests lay
|
||||
across 13 major scientific disciplines or 554 sub-disciplines, and will
|
||||
be able to see how these disciplines and sub-disciplines interrelate
|
||||
with one another on the map of science. Wireframes and design
|
||||
documentation for upcoming enhanced versions of the 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
|
||||
download.
|
||||
</p>
|
||||
<p>
|
||||
Several visualization also now provide a caching feature that improves
|
||||
performance after the initial processing.
|
||||
</p>
|
||||
<h4>QR Codes</h4>
|
||||
Pages for people in VIVO have the option of displaying QR codes.
|
||||
<br>
|
||||
<p>
|
||||
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>
|
||||
<ul>
|
||||
<li>
|
||||
support for certifications and licenses
|
||||
support for certifications and licenses
|
||||
</li>
|
||||
<li>
|
||||
expanded support for intellectual property (patents) (it was
|
||||
there as stub before but didn't allow common things such as assignee
|
||||
and issuer)
|
||||
expanded support for intellectual property (patents) (it was
|
||||
there as stub before but didn't allow common things such as assignee
|
||||
and issuer)
|
||||
</li>
|
||||
<li>
|
||||
support for editorial, reviewing and organizing activities
|
||||
support for editorial, reviewing and organizing activities
|
||||
</li>
|
||||
<li>
|
||||
expanded shared geographical instance data vocabulary to include
|
||||
the 50 U.S. states
|
||||
expanded shared geographical instance data vocabulary to include
|
||||
the 50 U.S. states
|
||||
</li>
|
||||
<li>
|
||||
representing specific types of EducationalTraining:
|
||||
PostdoctoralTraining, Internship, MedicalResidency
|
||||
representing specific types of EducationalTraining:
|
||||
PostdoctoralTraining, Internship, MedicalResidency
|
||||
</li>
|
||||
</ul>
|
||||
<h4>Linked open data</h4>
|
||||
Responses to linked data requests have been enhanced to include
|
||||
additional context about any individual, in working toward a goal of
|
||||
being able to provide all the data in a person's profile available as
|
||||
RDF via a single web request.
|
||||
<br>
|
||||
<p>
|
||||
Responses to linked data requests have been enhanced to include
|
||||
additional context about any individual, in working toward a goal of
|
||||
being able to provide all the data in a person's profile available as
|
||||
RDF via a single web request.
|
||||
</p>
|
||||
<br>
|
||||
<hr><!-- Page break --><!-- Installation process for V1.2 --><h2 id="installation">Installation process for V1.3</h2>
|
||||
<p>
|
||||
|
|
@ -129,9 +145,9 @@
|
|||
<ul>
|
||||
<li>
|
||||
These instructions assume that you are performing a clean
|
||||
install, including emptying an existing database, emptying the VIVO
|
||||
home directory, and removing a previous installation from the Tomcat
|
||||
webapps directory. Product functionality may not be as expected if you
|
||||
install, including emptying an existing database, emptying the VIVO
|
||||
home directory, 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>
|
||||
<li>
|
||||
|
|
@ -140,8 +156,8 @@
|
|||
</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>
|
||||
<h3>Where does VIVO live on your computer?</h3>
|
||||
|
|
@ -159,31 +175,31 @@
|
|||
<h4>VIVO inside Tomcat</h4>
|
||||
<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
|
||||
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
|
||||
VIVO, make the changes in the distribution directory, and run the build
|
||||
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
|
||||
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>
|
||||
in the deploy.properties file (see <a href="#deploy_properties">Step V</a>,
|
||||
below).
|
||||
</p>
|
||||
<h4>The VIVO home directory</h4>
|
||||
<p>
|
||||
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.
|
||||
You can create this wherever you choose. Tell VIVO where to find the
|
||||
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.
|
||||
You can create this wherever you choose. Tell VIVO where to find the
|
||||
home directory by setting <code>vitro.home.directory</code>
|
||||
in the
|
||||
deploy.properties file (see <a href="#deploy_properties">Step V</a>,
|
||||
below). You must create this directory before starting VIVO, and you
|
||||
must ensure that Tomcat has permission to read and write to this
|
||||
deploy.properties file (see <a href="#deploy_properties">Step V</a>,
|
||||
below). You must create this directory before starting VIVO, and you
|
||||
must ensure that Tomcat has permission to read and write to this
|
||||
directory when it runs.
|
||||
</p>
|
||||
<h4>The MySQL database</h4>
|
||||
<p>
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
occasionally through the MySQL client application.
|
||||
</p>
|
||||
<toc>
|
||||
|
|
@ -228,6 +244,9 @@
|
|||
<li>
|
||||
<a href="#installation_check">Was the installation successful?</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="#termsofuse">Review the VIVO Terms of Use</a>
|
||||
</li>
|
||||
</ol>
|
||||
</toc>
|
||||
<h3 id="required_software">I. Install required software </h3>
|
||||
|
|
@ -253,14 +272,14 @@
|
|||
<p>
|
||||
Be sure to set up the environment variables for <code java_home="">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 websites.
|
||||
</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
|
||||
* 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
|
||||
higher. Using unsupported versions may result in strange error messages
|
||||
related to table formatting or other unexpected problems.
|
||||
</p>
|
||||
<p>
|
||||
|
|
@ -270,13 +289,13 @@
|
|||
<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
|
||||
create the database and user with these commands substituting your
|
||||
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
|
||||
of
|
||||
the
|
||||
Most
|
||||
of
|
||||
the
|
||||
time, the hostname will equal <code>localhost</code>.
|
||||
</p>
|
||||
<pre> CREATE DATABASE dbname CHARACTER SET utf8;<br></pre>
|
||||
|
|
@ -292,8 +311,8 @@
|
|||
<br>
|
||||
</h3>
|
||||
<p>
|
||||
Download the VIVO application source as either <code>rel-1.2.zip</code>
|
||||
or <code>rel-1.2.gz</code>
|
||||
Download the VIVO application source as either <code>rel-1.3.zip</code>
|
||||
or <code>rel-1.3.gz</code>
|
||||
file and unpack it on your web server:
|
||||
<br>
|
||||
<a href="http://vivoweb.org/download">http://vivoweb.org/download</a>
|
||||
|
|
@ -306,15 +325,15 @@
|
|||
</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
|
||||
set two additional properties in this file. See the section below
|
||||
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>.
|
||||
</p>
|
||||
|
|
@ -354,8 +373,8 @@
|
|||
</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>
|
||||
|
|
@ -397,8 +416,8 @@
|
|||
<td colspan="2">
|
||||
URL of Solr context used in local VIVO search.
|
||||
Should consist of:<pre> scheme + servername + port + vivo_webapp_name + "solr"</pre>
|
||||
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
|
||||
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
|
||||
VIVO webapp.name (specified above) + "solr"
|
||||
</td>
|
||||
</tr>
|
||||
|
|
@ -412,25 +431,24 @@
|
|||
</tr>
|
||||
<tr>
|
||||
<td colspan="2">
|
||||
Restricts access to the Solr search platform.
|
||||
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
|
||||
Restricts access to the Solr search platform.
|
||||
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
|
||||
patterns, or the request will be rejected.
|
||||
<br>
|
||||
Examples:
|
||||
<code>
|
||||
<ul>
|
||||
<li>
|
||||
vitro.local.solr.ipaddress.mask = 127\.0\.0\.1
|
||||
</li>
|
||||
<li>
|
||||
vitro.local.solr.ipaddress.mask =
|
||||
127\.0\.0\.1,0:0:0:0:0:0:0:1
|
||||
</li>
|
||||
<li>
|
||||
vitro.local.solr.ipaddress.mask = 169.254.*
|
||||
</li>
|
||||
</ul>
|
||||
Examples:<code>
|
||||
<ul>
|
||||
<li>
|
||||
vitro.local.solr.ipaddress.mask = 127\.0\.0\.1
|
||||
</li>
|
||||
<li>
|
||||
vitro.local.solr.ipaddress.mask =
|
||||
127\.0\.0\.1,0:0:0:0:0:0:0:1
|
||||
</li>
|
||||
<li>
|
||||
vitro.local.solr.ipaddress.mask = 169.254.*
|
||||
</li>
|
||||
</ul>
|
||||
</code>
|
||||
</td>
|
||||
</tr>
|
||||
|
|
@ -444,9 +462,9 @@
|
|||
</tr>
|
||||
<tr>
|
||||
<td colspan="2">
|
||||
Directory where the VIVO application will store
|
||||
the data that it creates. This includes uploaded files (usually images)
|
||||
and the Solr search index. Be sure this directory exists and is
|
||||
Directory where the VIVO application will store
|
||||
the data that it creates. This includes uploaded files (usually images)
|
||||
and the Solr search index. Be sure this directory exists and is
|
||||
writable by the user who the Tomcat service is running as.
|
||||
</td>
|
||||
</tr>
|
||||
|
|
@ -460,9 +478,9 @@
|
|||
</tr>
|
||||
<tr>
|
||||
<td colspan="2">
|
||||
Specify an SMTP host that the application will
|
||||
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
|
||||
Specify an SMTP host that the application will
|
||||
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
|
||||
changes to their accounts.
|
||||
</td>
|
||||
</tr>
|
||||
|
|
@ -478,9 +496,9 @@
|
|||
<td colspan="2">
|
||||
Specify an email address which will appear as
|
||||
the sender in e-mail notifications to users (Optional). If a user
|
||||
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
|
||||
notice. If this is left blank, users will not be notified of changes to
|
||||
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
|
||||
notice. If this is left blank, users will not be notified of changes to
|
||||
their accounts.
|
||||
</td>
|
||||
</tr>
|
||||
|
|
@ -536,25 +554,9 @@
|
|||
</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>
|
||||
<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
|
||||
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>
|
||||
</tr>
|
||||
|
|
@ -568,8 +570,8 @@
|
|||
</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>
|
||||
|
|
@ -584,9 +586,9 @@
|
|||
<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
|
||||
SQLServer. Refer to http://openjena.org/wiki/SDB/Databases_Supported
|
||||
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>
|
||||
</tr>
|
||||
|
|
@ -600,9 +602,9 @@
|
|||
</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
|
||||
for this driver must be added to the the webapp/lib directory within
|
||||
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>
|
||||
</tr>
|
||||
|
|
@ -616,8 +618,8 @@
|
|||
</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>
|
||||
|
|
@ -636,9 +638,9 @@
|
|||
temporary password of 'rootPassword'. You will be prompted to create a
|
||||
new password on first login.
|
||||
<p>
|
||||
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
|
||||
root user. It is best to create a Site Admin account to use for every
|
||||
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
|
||||
root user. It is best to create a Site Admin account to use for every
|
||||
day administrative tasks.
|
||||
</p>
|
||||
</td>
|
||||
|
|
@ -653,9 +655,9 @@
|
|||
</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
|
||||
name that matches the value of this property, the user will be
|
||||
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>
|
||||
</tr>
|
||||
|
|
@ -667,15 +669,33 @@
|
|||
http://vivo.mydomain.edu/ns#networkId
|
||||
</td>
|
||||
</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>
|
||||
<td colspan="2">
|
||||
The temporal graph visualization can require
|
||||
extensive machine resources. This can have a particularly noticable
|
||||
impact on memory usage if
|
||||
<ul>
|
||||
<li>
|
||||
VIVO is configured to use Jena SDB,
|
||||
</li>
|
||||
<li>
|
||||
The organization tree is deep,
|
||||
</li>
|
||||
|
|
@ -683,11 +703,8 @@
|
|||
The number of grants and publications is large.
|
||||
</li>
|
||||
</ul>
|
||||
The VIVO developers are working to make this visualization more
|
||||
efficient. In the meantime, VIVO release 1.2 guards against this impact
|
||||
by disabling the temporal graph visualization unless the
|
||||
"visualization.temporal" flag is set to "enabled". To enable it,
|
||||
uncomment the line for this setting.
|
||||
VIVO V1.3 mitigates this problem by the way of a caching
|
||||
mechanism and hence we can safely set this to be enabled by default.
|
||||
</td>
|
||||
</tr>
|
||||
<tr class="odd_row">
|
||||
|
|
@ -706,9 +723,9 @@
|
|||
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
|
||||
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
|
||||
default whenever the temporal graph visualization is rendered without
|
||||
being passed an explicit org. For example, to use "Ponce School of
|
||||
want to identify as the top level organization. It will be used as the
|
||||
default whenever the temporal graph visualization is rendered without
|
||||
being passed an explicit org. For example, to use "Ponce School of
|
||||
Medicine" as the top organization:
|
||||
<br>
|
||||
<code>visualization.topLevelOrg =
|
||||
|
|
@ -752,14 +769,14 @@
|
|||
<h3 id="tomcat_settings">VI. 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 database are 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
|
||||
"setenv.bat" file in Tomcat's bin directory is a convenient place to
|
||||
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. <em>If this file does not exist in Tomcat's
|
||||
bin directory, you can create it.</em>
|
||||
<br>
|
||||
|
|
@ -769,9 +786,9 @@
|
|||
<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
|
||||
is preferable. For testing with small sets of data, 256m to 512m should
|
||||
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>
|
||||
<p>
|
||||
|
|
@ -779,9 +796,9 @@
|
|||
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
|
||||
default configuration. Ensure that your installation can support the
|
||||
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>
|
||||
|
|
@ -790,39 +807,39 @@
|
|||
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
|
||||
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
|
||||
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 files in Tomcat's logs directory. Error messages are commonly found
|
||||
in <code>catalina.out</code>
|
||||
or <code>localhost.log</code>
|
||||
</p>
|
||||
<h3 id="add_rdf">VIII. 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
|
||||
<p>
|
||||
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>rootUser.emailAddress</code>
|
||||
you set up in Step IV. The initial password for the root account is
|
||||
"rootPassword" (without the quotes). On first login, you will be
|
||||
you set up in Step IV. The initial password for the root account is
|
||||
"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
|
||||
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
|
||||
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
|
||||
complete functionality throughout the site.
|
||||
</p>
|
||||
<p>
|
||||
After logging in, 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 are a number of visibility and display
|
||||
options available for each ontology entity. VIVO comes with a core VIVO
|
||||
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
|
||||
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 from a file on your local machine.
|
||||
Ensure that the "add RDF" radio button is selected. You will also
|
||||
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.
|
||||
Ensure that the "add RDF" radio button is selected. You will also
|
||||
likely want to check "create classgroups automatically."
|
||||
</p>
|
||||
<p>
|
||||
|
|
@ -837,29 +854,29 @@
|
|||
"Contact Us" form)</h3>
|
||||
<p>
|
||||
If you have configured your application to use the "Contact Us"
|
||||
feature in Step IV (<code>email.smtpHost</code>), you will also need to
|
||||
add an email address to the VIVO application. This is the email
|
||||
to which the contact form will submit. It can be a list server or an
|
||||
feature in Step IV (<code>email.smtpHost</code>), you will also need to
|
||||
add an email address to the VIVO application. This is the email
|
||||
to which the contact form will submit. 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
|
||||
Editing Form," enter a functional email address in the field "Contact
|
||||
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>email.smtpHost</code>
|
||||
in Step IV and do NOT
|
||||
provide an email address in this step, your users will receive a java
|
||||
in Step IV and do NOT
|
||||
provide an email address in this step, your users will receive a java
|
||||
error in the interface.
|
||||
</p>
|
||||
<h3 id="tomcat_connector">X. 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.
|
||||
8080) and an additional reference to the Tomcat context name (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>
|
||||
<p>
|
||||
|
|
@ -878,9 +895,9 @@
|
|||
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
|
||||
to
|
||||
requests from Apache via the connector. Look for the
|
||||
respond
|
||||
to
|
||||
requests from Apache via the connector. Look for the
|
||||
<connector> directive and add the following properties:
|
||||
</p>
|
||||
<pre> connectionTimeout="20000" maxThreads="320" keepAliveTimeout="20000" <br> </pre>
|
||||
|
|
@ -904,15 +921,15 @@
|
|||
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
|
||||
system. When the user completes the authentication, the Apache server
|
||||
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
|
||||
will try to find a page associated with the user. If such a page is
|
||||
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>
|
||||
<h4>Configuring the Apache server</h4>
|
||||
|
|
@ -940,9 +957,9 @@
|
|||
<h5>The name of the HTTP header that will hold the external user's
|
||||
network ID.</h5>
|
||||
<p>
|
||||
When a user completes the authentication process, the Apache
|
||||
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
|
||||
When a user completes the authentication process, the Apache
|
||||
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
|
||||
which header is used for this purpose.
|
||||
</p>
|
||||
<p>
|
||||
|
|
@ -979,9 +996,9 @@
|
|||
<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
|
||||
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
|
||||
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
|
||||
untyped literal). You need to tell VIVO what property should be used
|
||||
for matching. Insert a line like this in the deploy.properties file:
|
||||
</p>
|
||||
<pre>selfEditing.idMatchingProperty = [the URI of the property]</pre>
|
||||
|
|
@ -1016,9 +1033,9 @@
|
|||
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
|
||||
ontology files and building the index took more than 5 minutes from the
|
||||
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>
|
||||
<li>
|
||||
|
|
@ -1038,30 +1055,30 @@
|
|||
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
|
||||
taken to the "Individual Control Panel." Make note of the value of the
|
||||
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
|
||||
pink
|
||||
box on that page enter the URI of the individual you
|
||||
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" is followed by "failed (400)" you are not successfully
|
||||
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>
|
||||
</ul>
|
||||
|
|
@ -1071,18 +1088,32 @@
|
|||
<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
|
||||
Australia itself. To trigger the search index, you can log in as a site
|
||||
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>
|
||||
</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>
|
||||
<!-- #wrapper-content -->
|
||||
<div id="footer" role="contentinfo">
|
||||
<p class="copyright">
|
||||
<small>
|
||||
©2011 All Rights Reserved | <a class="terms" href="/termsOfUse">Terms of Use</a>
|
||||
©2011 All Rights Reserved
|
||||
</small>
|
||||
| Powered
|
||||
by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a>
|
||||
|
|
|
|||
|
|
@ -14,7 +14,7 @@
|
|||
<div id="wrapper-content" role="main">
|
||||
<h1>VIVO Release 1 V1.3 Upgrade Guide</h1>
|
||||
<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>
|
||||
<toc>
|
||||
<ul>
|
||||
|
|
@ -61,30 +61,30 @@
|
|||
</p>
|
||||
<h4>Authorization</h4>
|
||||
<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
|
||||
configuration and editing. The first phase of the new user account
|
||||
interface is included in V1.3. This interface provides a user search, a
|
||||
root acount, and password reset functionality where the password gets
|
||||
emailed to the user. The next phase will provide the ability to create
|
||||
configuration and editing. The first phase of the new user account
|
||||
interface is included in V1.3. This interface provides a user search, a
|
||||
root acount, and password reset functionality where the password gets
|
||||
emailed to the user. The next phase will provide the ability to create
|
||||
new roles.
|
||||
</p>
|
||||
<h4>Menu management</h4>
|
||||
<p>
|
||||
The menus across the top of the site (Home, People, Organizations,
|
||||
Research, Events) can now be managed in a web form instead of editing
|
||||
an RDF file. In addition to making site management much easier,
|
||||
form-based editing also allows more control over what classes of data
|
||||
are displayed and provides a mechanism to limit certain menu pages to
|
||||
Research, Events) can now be managed in a web form instead of editing
|
||||
an RDF file. In addition to making site management much easier,
|
||||
form-based editing also allows more control over what classes of data
|
||||
are displayed and provides a mechanism to limit certain menu pages to
|
||||
content identified as internal to the institution.
|
||||
</p>
|
||||
<h4>FreeMarker template improvements</h4>
|
||||
<p>
|
||||
While less directly visible to the public, V1.3 also includes
|
||||
additional changes focused directly on supporting open source community
|
||||
involvement in extending and customizing VIVO. The development team
|
||||
began a year ago to transition VIVO's code base away from Java Server
|
||||
Pages to the FreeMarker page templating system that much more cleanly
|
||||
additional changes focused directly on supporting open source community
|
||||
involvement in extending and customizing VIVO. The development team
|
||||
began a year ago to transition VIVO's code base away from Java Server
|
||||
Pages to the FreeMarker page templating system that much more cleanly
|
||||
separates internal application programming logic from page display.
|
||||
</p>
|
||||
<h4>Visualization</h4>
|
||||
|
|
@ -93,12 +93,12 @@
|
|||
which allows users to visually explore the scientific strengths of a
|
||||
university, school, department, or person in the VIVO instance. Users
|
||||
will be able to see where an organization or person's interests lay
|
||||
across 13 major scientific disciplines or 554 sub-disciplines, and will
|
||||
across 13 major scientific disciplines or 554 sub-disciplines, and will
|
||||
be able to see how these disciplines and sub-disciplines interrelate
|
||||
with one another on the Map of Science. Wireframes and design
|
||||
documentation for upcoming enhanced versions of the 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
|
||||
with one another on the Map of Science. Wireframes and design
|
||||
documentation for upcoming enhanced versions of 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
|
||||
download.
|
||||
</p>
|
||||
<p>
|
||||
|
|
@ -227,10 +227,10 @@
|
|||
</li>
|
||||
<li>
|
||||
DO NOT reinstall MySQL or recreate the MySQL database. Please
|
||||
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
|
||||
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
|
||||
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
|
||||
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.
|
||||
</li>
|
||||
<li>
|
||||
|
|
@ -238,10 +238,10 @@
|
|||
</li>
|
||||
<li>
|
||||
First-time login of the administrator account after the
|
||||
upgrade
|
||||
process is complete will use the password previously set, NOT the
|
||||
default password used on the first login after the initial
|
||||
installation. With V1.3 there is also a new root user. Please see the
|
||||
upgrade
|
||||
process is complete will use the password previously set, NOT the
|
||||
default password used on the first login after the initial
|
||||
installation. With V1.3 there is also a new root user. Please see the
|
||||
section on <a href="#authorization">Authorization changes</a>
|
||||
for more
|
||||
information.
|
||||
|
|
@ -269,20 +269,20 @@
|
|||
queries are issued directly against the underlying database. This
|
||||
allows VIVO installations to display data from large RDF models while
|
||||
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
|
||||
parameters of the database server. Additionally, advanced OWL reasoning
|
||||
(not enabled by default in either mode) is not possible in SDB mode.
|
||||
With SDB, only the default set of inferences (inferred rdf:type
|
||||
statements) are generated, and they are generated as soon as data is
|
||||
parameters of the database server. Additionally, advanced OWL reasoning
|
||||
(not enabled by default in either mode) is not possible in SDB mode.
|
||||
With SDB, only the default set of inferences (inferred rdf:type
|
||||
statements) are generated, and they are generated as soon as data is
|
||||
edited rather than in a background process.
|
||||
</p>
|
||||
<p>
|
||||
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
|
||||
(roughly a million triples or more). You can start the conversion
|
||||
process in the background while the RDB system is running. This will
|
||||
reduce the delay in initial startup after the application is redeployed
|
||||
complete if the installation contains a large amount of RDF data
|
||||
(roughly a million triples or more). You can start the conversion
|
||||
process in the background while the RDB system is running. This will
|
||||
reduce the delay in initial startup after the application is redeployed
|
||||
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
|
||||
while this background conversion is running</span>.
|
||||
|
|
@ -298,12 +298,12 @@
|
|||
</p>
|
||||
<p>
|
||||
During the course of the SDB setup, which may take several hours
|
||||
on
|
||||
on
|
||||
a large database, subsequent requests to /sdbsetup will display a
|
||||
message that the operation is still in progress. When a request for
|
||||
this page shows a message that the SDB setup has completed
|
||||
successfully, shut down Tomcat, set deploy.properties to SDB mode,
|
||||
redeploy, and restart Tomcat. VIVO will now be running from the SDB
|
||||
message that the operation is still in progress. When a request for
|
||||
this page shows a message that the SDB setup has completed
|
||||
successfully, shut down Tomcat, set deploy.properties to SDB mode,
|
||||
redeploy, and restart Tomcat. VIVO will now be running from the SDB
|
||||
store.
|
||||
</p>
|
||||
<p>
|
||||
|
|
@ -364,21 +364,21 @@
|
|||
<toc>
|
||||
<ul>
|
||||
<li>
|
||||
The file used to register list views has changed to a directory where new
|
||||
<code>.rdf</code> or <code>.n3</code> files can be placed:
|
||||
<code>/vivo/productMods/WEB-INF/ontologies/app/loadedAtStartup</code>. The rdf required
|
||||
The file used to register list views has changed to a directory where new<code>.rdf</code>
|
||||
or <code>.n3</code>
|
||||
files can be placed: <code>/vivo/productMods/WEB-INF/ontologies/app/loadedAtStartup</code>. The rdf required
|
||||
to register a new view has not changed.
|
||||
</li>
|
||||
<li>
|
||||
<code><query-base></code> and <code><query-collated></code>
|
||||
<code><query-base></code>
|
||||
and <code><query-collated></code>
|
||||
have been replaced with a single query <code><query-select></code>
|
||||
that contains tags for fragments to be used only in the collated
|
||||
version of the query.
|
||||
</li>
|
||||
</ul>
|
||||
<p>
|
||||
These and other changes are documented in greater detail in
|
||||
<code style="whitespace:nowrap;">/vitro/doc/list_view_configuration_guidelines.txt</code>.
|
||||
These and other changes are documented in greater detail in<code style="whitespace:nowrap;">/vitro/doc/list_view_configuration_guidelines.txt</code>.
|
||||
</p>
|
||||
</toc>
|
||||
<h4 id="authorization">v. Authorization</h4>
|
||||
|
|
@ -507,23 +507,23 @@
|
|||
<dl style="margin-left: 40px;">
|
||||
<dd>
|
||||
<p>
|
||||
If you are upgrading to VIVO V1.3 from an existing
|
||||
If you are upgrading to VIVO V1.3 from an existing
|
||||
VIVO
|
||||
installation, the user accounts in your system will be migrated into
|
||||
the new data structures. When migrating an account, both 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
|
||||
installation, the user accounts in your system will be migrated into
|
||||
the new data structures. When migrating an account, both 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
|
||||
behave as the old account did.
|
||||
</p>
|
||||
<p>
|
||||
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>.
|
||||
You
|
||||
You
|
||||
should
|
||||
plan
|
||||
for
|
||||
this
|
||||
as
|
||||
plan
|
||||
for
|
||||
this
|
||||
as
|
||||
part of your migration to V1.3
|
||||
</p>
|
||||
</dd>
|
||||
|
|
@ -552,10 +552,10 @@
|
|||
<blockquote>
|
||||
<strong>Note:</strong>
|
||||
when creating the account,
|
||||
the
|
||||
administrator may indicate that it will only be used with an external
|
||||
authentication system like Shibboleth or CUWebAuth. In this case, the
|
||||
account will not require a password, and the e-mail notification
|
||||
the
|
||||
administrator may indicate that it will only be used with an external
|
||||
authentication system like Shibboleth or CUWebAuth. In this case, the
|
||||
account will not require a password, and the e-mail notification
|
||||
message to the user will not provide a password link.
|
||||
</blockquote>
|
||||
<p>
|
||||
|
|
@ -625,12 +625,12 @@
|
|||
<div style="margin-left: 40px;">
|
||||
The password for this account is
|
||||
automatically set to <code>rootPassword</code>,
|
||||
but
|
||||
but
|
||||
you
|
||||
will
|
||||
be
|
||||
required
|
||||
to change the password the first time you log
|
||||
will
|
||||
be
|
||||
required
|
||||
to change the password the first time you log
|
||||
in.
|
||||
</div>
|
||||
<blockquote style="margin-left: 40px;">
|
||||
|
|
@ -641,11 +641,11 @@
|
|||
<p style="margin-left: 40px;">
|
||||
The root account is not a site
|
||||
administrator's account — it
|
||||
is
|
||||
is
|
||||
more powerful than a site administrator's account. The root account is
|
||||
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
|
||||
root account can be very useful and rather dangerous. It can also give
|
||||
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
|
||||
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
|
||||
shown here which ins not visible to other accounts.
|
||||
</p>
|
||||
|
|
@ -665,10 +665,10 @@
|
|||
</p>
|
||||
<p>
|
||||
2. Create a new deploy.properties using the same values as in
|
||||
your
|
||||
previous installation and set values for the new variables as described
|
||||
below (vitro.local.solr.url, vitro.local.solr.ipaddress.mask,
|
||||
vitro.home.directory, email.smptHost, email.replyTo,
|
||||
your
|
||||
previous installation and set values for the new variables as described
|
||||
below (vitro.local.solr.url, vitro.local.solr.ipaddress.mask,
|
||||
vitro.home.directory, email.smptHost, email.replyTo,
|
||||
rootUser.emailAddress)
|
||||
<br>
|
||||
</p>
|
||||
|
|
@ -835,10 +835,10 @@
|
|||
<tr>
|
||||
<td colspan="2">
|
||||
Specify an email address which will appear as
|
||||
the sender in e-mail notifications to users (Optional). If a user
|
||||
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
|
||||
notice. If this is left blank, users will not be notified of changes to
|
||||
the sender in e-mail notifications to users (Optional). If a user
|
||||
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
|
||||
notice. If this is left blank, users will not be notified of changes to
|
||||
their accounts.
|
||||
</td>
|
||||
</tr>
|
||||
|
|
@ -893,23 +893,6 @@
|
|||
password
|
||||
</td>
|
||||
</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>
|
||||
<td colspan="2">
|
||||
Specify the maximum number of active
|
||||
|
|
@ -1022,15 +1005,33 @@
|
|||
http://vivo.mydomain.edu/ns#networkId
|
||||
</td>
|
||||
</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>
|
||||
<td colspan="2">
|
||||
The temporal graph visualization can require
|
||||
extensive machine resources. This can have a particularly noticable
|
||||
impact on memory usage if
|
||||
<ul>
|
||||
<li>
|
||||
VIVO is configured to use Jena SDB,
|
||||
</li>
|
||||
<li>
|
||||
The organization tree is deep,
|
||||
</li>
|
||||
|
|
@ -1055,12 +1056,12 @@
|
|||
The temporal graph visualization is used to
|
||||
compare different organizations/people within an organization on
|
||||
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
|
||||
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
|
||||
default whenever the temporal graph visualization is rendered without
|
||||
being passed an explicit org. For example, to use "Ponce School of
|
||||
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
|
||||
default whenever the temporal graph visualization is rendered without
|
||||
being passed an explicit org. For example, to use "Ponce School of
|
||||
Medicine" as the top organization:
|
||||
<br>
|
||||
<code>visualization.topLevelOrg =
|
||||
|
|
@ -1078,7 +1079,7 @@
|
|||
</tr>
|
||||
<tr>
|
||||
<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.
|
||||
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.
|
||||
|
|
@ -1121,10 +1122,10 @@
|
|||
the theme:<pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre>
|
||||
A sample <code>googleAnalytics.ftl</code>
|
||||
is included in the built-in
|
||||
theme. This file serves only as an example, and you must replace the
|
||||
tracking code shown with your institution's own tracking code. For
|
||||
additional information about the GATC for the NIH-funded VIVO
|
||||
implementation sites and a copy of your institution's tracking code,
|
||||
theme. This file serves only as an example, and you must replace the
|
||||
tracking code shown with your institution's own tracking code. For
|
||||
additional information about the GATC for the NIH-funded VIVO
|
||||
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
|
||||
Google
|
||||
Analytics
|
||||
|
|
@ -1222,10 +1223,10 @@
|
|||
</p>
|
||||
<p>
|
||||
When Apache Tomcat starts up following the upgrade, it will
|
||||
initiate a process to examine the knowledge base and apply necessary
|
||||
changes. Not all of the modifications that may be required can be
|
||||
automated, so manual review of the knowledge base is recommended after
|
||||
the automated upgrade process. The automated process will make only the
|
||||
initiate a process to examine the knowledge base and apply necessary
|
||||
changes. Not all of the modifications that may be required can be
|
||||
automated, so manual review of the knowledge base is recommended after
|
||||
the automated upgrade process. The automated process will make only the
|
||||
following types of changes:
|
||||
</p>
|
||||
<dl>
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue