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<!DOCTYPE html>
< html lang = "en" >
< head >
< meta charset = "utf-8" / >
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< title > VIVO Release 1 V1.2 Upgrade Guide< / title >
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< link rel = "stylesheet" href = "./css/doc.css" media = "screen" / >
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< / head >
< body >
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< div id = "branding" role = "banner" >
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< h1 class = "vivo-logo" > < a href = "/" > < span class = "displace" > VIVO< / span > < / a > < / h1 >
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< / div >
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<!-- Start of content -->
< div id = "wrapper-content" role = "main" >
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< h1 > VIVO Release 1 v1.2 Upgrade Guide< / h1 >
< small >
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February 16, 2011 - Upgrading from Release 1 v1.1 to Release 1
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v1.2
< / small >
< toc >
< ul >
< li >
< a href = "#announcement" > Release announcement for V1.2< / a >
< / li >
< li >
< a href = "#upgrade" > Upgrade process for V1.2< / a >
< / li >
< / ul >
< / toc >
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< p >
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This document provides a short description of the steps involved in
upgrading your installation of VIVO from Release 1, Version 1.1 to
Version 1.2. This and other documentation can be found on the < a href = "http://vivoweb.org/support" > support page< / a >
at < a href = "http://vivoweb.org" > VIVOweb.org< / a >
< / p >
< p >
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If you need to do a fresh install, please consult the VIVO Release 1 v1.2
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Installation Guide found on < a href = "http://vivoweb.org/support" > vivoweb.org< / a >
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or the install.html file located in the < code > doc< / code >
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directory of the VIVO source code distribution. The installation
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document also has a list of the required software and versions.
< / p >
<!-- Release Announcement --> < h2 id = "announcement" > Release anouncement for V1.2< / h2 >
< p >
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The VIVO 1.2 release incorporates major changes throughout the application -
notably a new templating system to support more versatile page rendering, plus
improvements to address scalability. The release also features a new personal
visualization option covering 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 > .
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< / p >
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< h4 > Templating system for page generation, navigation, and theming< / h4 >
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< p >
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A fresh installation of VIVO 1.2 looks strikingly different, with the introduction
of a new default theme which takes advantage of the navigation and browse features
delivered by the templating system. Individual pages now offer inline navigation to
streamline viewing of expanded personal and organizational profiles, as well as
improved content layout and organization. New browse controls on the home page and
menu pages help 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.
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< / p >
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< h4 > Storage model< / h4 >
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< p >
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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.
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< / p >
< p >
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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.
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< / p >
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< h4 > New visualizations< / h4 >
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< p >
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Visualizations of networks of co-authors are now complemented by visualizations of co-investigators
on grants, with similar interactivity and options for export as images or data.
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< / p >
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< h4 > Ontology< / h4 >
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< p >
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VIVO 1.2 includes a new ontology module representing research
resources including biological specimens, human studies, instruments,
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organisms, protocols, reagents, and research opportunities. This module
is aligned with the top-level ontology classes and properties from the
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NIH-funded < a href = "https://www.eagle-i.org/home/" > eagle-i Project< / a > .
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< / p >
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< h3 > Associated VIVO releases< / h3 >
< h4 > VIVO Harvester< / h4 >
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< p >
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The Harvester development team is releasing version 1.0 of the VIVO Harvester library shortly
following the release of VIVO 1.2. The Harvester is an extensible data ingest and updating
framework with sample configurations for loading PubMed publication, grants, and human resources
data. Pre-release versions of the Harvester are available at
< a href = "http://sourceforge.net/projects/vivo" > http://sourceforge.net/projects/vivo< / a > .
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< / p >
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< hr > <!-- Page break --> <!-- Upgrade process for V1.2 --> < h2 id = "upgrade" > Upgrade process for V1.2< / h2 >
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< toc >
< ol class = "roman1" >
< li >
< a href = "#preparation" > Before Performing the Upgrade< / a >
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< / li >
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< li >
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< a href = "#triple_store" > Chose Triple Store< / a >
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< / li >
< li >
< a href = "#upgrade_process" > The Upgrade Process< / a >
< / li >
< li >
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< a href = "#ontology" > Ontology Changes< / a >
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< ol class = "roman2" >
< li >
< a href = "#verify_ontology_upgrade" > Verify Ontology upgrade
process< / a >
< / li >
< li >
< a href = "#ontology_knowledge_base" > Ontology knowledge base
manual review< / a >
< / li >
< / ol >
< / li >
< li >
< a href = "#fileSystem" > File Storage System Upgrade< / a >
< ol class = "roman2" >
< li >
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< a href = "#changes_to_storage" > Changes to the File
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Storage System< / a >
< / li >
< li >
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< a href = "#verify_file_upgrade" > Verify File Storage
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System upgrade process< / a >
< / li >
< / ol >
< / li >
< li >
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< a href = "#theme" > Theme Changes< / a >
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< / li >
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< li >
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< a href = "#setup_sdb" > Set Up SDB Store in the Background (Optional)< / a >
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< / li >
< / ol >
< / toc >
< h3 id = "preparation" > I. Before Performing the Upgrade< / h3 >
< p >
Please ensure that backups are created of the:
< / p >
< ul style = "list-style-type: square;" >
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< li >
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Tomcat webapps directory
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< / li >
< li >
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Original source directory
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< / li >
< li >
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MySQL database (mysqldump)
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< / li >
< / ul >
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< p >
The upgrade process is similar to the original install process with
the following EXCEPTIONS:
< / p >
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< ul >
< li >
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DO NOT reinstall MySQL or recreate the MySQL database. Please
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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.
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< / li >
< li >
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It is not necessary to add RDF data.
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< / li >
< li >
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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.
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< / li >
< li >
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The first time Apache Tomcat starts up after the upgrade, it
will initiate a process that modifies the knowledge base to align the
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data with the revised ontology. See the section on the < a href = "#ontology" > Ontology Upgrade< / a >
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below for more information.
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< / li >
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< / ul >
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< h3 id = "triple_store" > II. Choose Triple Store< / h3 >
< p >
VIVO 1.2 offers a choice of two triple store technologies: in-memory models backed by
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Jena's legacy relational database store (RDB), and Jena's SPARQL database (SDB). RDB was
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used by VIVO 1.1.1 and earlier. This mode offers fast response, but only by caching the
entire RDF model in the server's main memory. The memory available to VIVO limits the
number of RDF statements that may be stored.
< / p >
< p >
SDB mode caches only a fraction of the RDF data in memory. Most 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 make 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, though they are generated as soon as data is edited rather than in a background process.
< / p >
< p >
Though a VIVO installation may be switched back and forth between RDB and SDB mode by changing
a configuration property and redeploying the application, it is important to note that data
added in one mode will not typically appear in the other. The exception is when a system is
first switched from RDB mode to SDB mode. In this case, the data from the RDB store will be
automatically migrated to SDB.
< / p >
< p >
A VIVO 1.2 system that is upgraded from VIVO 1.1.1 must initially be run in RDB mode in order
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to receive required ontology updates. Attempting to run an upgraded system initially in SDB will
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result in a logged error message, and the application will not start. After the system starts
up successfully the first time in RDB mode, it may then be switched to SDB, redeployed, and restarted.
Upon restart, the data in the RDB store will be copied to the SDB store.
< / p >
< p >
This copying process can take a number of hours to complete if the installation contains a large
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amount of RDF data (roughly a million triples or more). See section < a href = "#setup_sdb" > Set Up SDB Store in the Background (Optional)< / a >
for instructions on how
to run this lengthy conversion process in the background while an RDB system is operating.
Doing this will reduce the time necessary to start VIVO the first time it is run in SDB mode.
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< / p >
< h3 id = "upgrade_process" > III. The Upgrade Process< / h3 >
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< p >
1. Download the new distribution file and unpack it into a new
source directory.
< / p >
< p >
2. Create deploy.properties, using the same values as in your
previous installation and set values for the new variables. The
following table shows the default properties for deploy.properties with
new V1.2 properties in < span class = "blue" > blue< / span > .<!-- deploy.properties table from install.html -->
< / p >
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< table >
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< tbody >
< tr >
< th >
Property Name
< / th >
< th >
Example Value
< / th >
< / tr >
< tr >
< td colspan = "2" >
Default namespace: VIVO installations make their
RDF resources available for harvest using linked data. Requests for RDF
resource URIs redirect to HTML or RDF representations as specified by
the client. To make this possible, VIVO's default namespace must have
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a certain structure and begin with the public web address of the VIVO
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installation. For example, if the web address of a VIVO installation is
"http://vivo.example.edu/" the default namespace must be set to
"http://vivo.example.edu/individual/" in order to support linked data.
Similarly, if VIVO is installed at "http://www.example.edu/vivo" the
default namespace must be set to
"http://www.example.edu/vivo/individual/"< h4 > * The namespace must end with "individual/" (including the
trailing slash).< / h4 >
< / td >
< / tr >
< tr class = "odd_row" >
< td >
Vitro.defaultNamespace
< / td >
< td >
http://vivo.mydomain.edu/individual/
< / td >
< / 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
setting to point elsewhere in development environments).
< / td >
< / tr >
< tr class = "odd_row" >
< td >
vitro.core.dir
< / td >
< td >
./vitro-core
< / td >
< / tr >
< tr >
< td colspan = "2" >
Directory where tomcat is installed.
< / td >
< / tr >
< tr class = "odd_row" >
< td >
tomcat.home
< / td >
< td >
/usr/local/tomcat
< / td >
< / tr >
< tr >
< td colspan = "2" >
Name of your VIVO application.
< / td >
< / tr >
< tr class = "odd_row" >
< td >
webapp.name
< / td >
< td >
vivo
< / td >
< / tr >
< tr >
< td colspan = "2" >
Directory where uploaded files will be stored.
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Be sure this directory exists and is writable by the user who
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the Tomcat service is running as.
< / td >
< / tr >
< tr class = "odd_row" >
< td >
upload.directory
< / td >
< td >
/usr/local/vivo/data/uploads
< / td >
< / tr >
< tr >
< td colspan = "2" >
Directory where the Lucene search index will be
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built. Be sure this directory exists and is writable by the user who
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the Tomcat service is running as.
< / td >
< / tr >
< tr class = "odd_row" >
< td >
LuceneSetup.indexDir
< / td >
< td >
/usr/local/vivo/data/luceneIndex
< / td >
< / 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
be hidden and disabled.
< / td >
< / tr >
< tr class = "odd_row" >
< td >
Vitro.smtpHost
< / td >
< td >
smtp.servername.edu
< / td >
< / tr >
< tr >
< td colspan = "2" >
Specify the JDBC URL of your database. Change
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the end of the URL to reflect your database name (if it is not "vivo").
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< / td >
< / tr >
< tr class = "odd_row" >
< td >
VitroConnection.DataSource.url
< / td >
< td >
jdbc:mysql://localhost/vivo
< / td >
< / tr >
< tr >
< td colspan = "2" >
Change the username to match the authorized user
you created in MySQL.
< / td >
< / tr >
< tr class = "odd_row" >
< td >
VitroConnection.DataSource.username
< / td >
< td >
username
< / td >
< / tr >
< tr >
< td colspan = "2" >
Change the password to match the password you
created in MySQL.
< / td >
< / tr >
< tr class = "odd_row" >
< td >
VitroConnection.DataSource.password
< / td >
< td >
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 blue" >
< td >
VitroConnection.DataSource.tripleStoreType
< / td >
< td >
SDB
< / td >
< / tr >
< tr >
< td colspan = "2" >
Specify the maximum number of active connections
in the database connection pool to support the anticipated number of
concurrent page requests. It is not necessary to adjust this value when
using the RDB configuration.
< / td >
< / tr >
< tr class = "odd_row blue" >
< td >
VitroConnection.DataSource.pool.maxActive
< / td >
< td >
40
< / td >
< / tr >
< tr >
< td colspan = "2" >
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 >
< tr class = "odd_row blue" >
< td >
VitroConnection.DataSource.pool.maxIdle
< / td >
< td >
10
< / td >
< / tr >
< tr >
< td colspan = "2" >
Change the dbtype setting to use a database
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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
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for additional information.
< / td >
< / tr >
< tr class = "odd_row blue" >
< td >
VitroConnection.DataSource.dbtype
< / td >
< td >
MySQL
< / td >
< / 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 < code > webapp/lib< / code >
directory within the vitro.core.dir specified above.
< / td >
< / tr >
< tr class = "odd_row blue" >
< td >
VitroConnection.DataSource.driver
< / td >
< td >
com.mysql.jdbc.Driver
< / td >
< / tr >
< tr >
< td colspan = "2" >
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 >
< tr class = "odd_row blue" >
< td >
VitroConnection.DataSource.validationQuery
< / td >
< td >
SELECT 1
< / td >
< / 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
of 'defaultAdmin'. You will be prompted to create a new password on
first login.
< / td >
< / tr >
< tr class = "odd_row" >
< td >
initialAdminUser
< / td >
< td >
defaultAdmin
< / td >
< / 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
authorized to edit that Individual. For example, to use the netID
at Cornell University as the property:
< br >
< span style = "font-style: italic;" > seflEditing.idMatchingProperty
=
http://vivo.cornell.edu/ns/hr/0.9/hr.owl#netId< / span >
< / td >
< / tr >
< tr class = "odd_row blue" >
< td >
selfEditing.idMatchingProperty
< / td >
< td >
http://vivo.mydomain.edu/ns#networkId
< / td >
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< / 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 >
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< li >
VIVO is configured to use Jena SDB,
< / li >
< li >
The organization tree is deep,
< / li >
< li >
The number of grants and publications is large.
< / li >
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< / ul >
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The VIVO developers are working to make this visualization more efficient.
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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.
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< / td >
< / tr >
< tr class = "odd_row blue" >
< td >
visualization.temporal
< / td >
< td >
enabled
< / td >
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< / tr >
< tr >
< td colspan = "2" >
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 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 Medicine" as the top
organization:
< br >
< span style = "font-style: italic;" > visualization.topLevelOrg =
http://vivo.psm.edu/individual/n2862< / span >
< / td >
< / tr >
< tr class = "odd_row blue" >
< td >
visualization.topLevelOrg
< / td >
< td >
http://vivo-trunk.indiana.edu/individual/topLevelOrgURI
< / td >
< / tr >
< / tbody >
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< / table >
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< p >
3. Apply any previous changes you have made to the new source
directory.
< / p >
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< blockquote >
< strong > Special notes regarding source files< / strong >
< ul >
< li >
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This process assumes any changes made to the application were
made in the source directory and deployed, and were not made directly
within the Tomcat webapps directory.
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< / li >
< li >
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In many cases, simply copying the modified files from your
original source directory will not work since the files on which they
are based have changed. It will be necessary to inspect the new source
files and add any changes to them at that time.
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< / li >
< li >
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NIH-funded VIVO implementations will need to apply the Google
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Analytics Tracking Code (GATC) to < code > googleAnalytics.ftl< / code >
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in the theme: < pre > [new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl< / pre >
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A sample < code > googleAnalytics.ftl< / code >
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is included in the built-in theme. This file serves only as an example,
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and you must replace the tracking code shown with your institution's own
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tracking code. For additional information about the GATC for the NIH-funded
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VIVO implementation sites and a copy of your institution's tracking code, see
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the < a href = "https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI" > VIVO Google Analytics wiki page< / a > .
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< / li >
< li >
If you had used the < code > vivo/contrib/FLShibboleth< / code >
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code in your previous release, you should stop using it. Consult < code > install.html< / code >
or < a href = "VIVO_Release-1-v1.2_Installation_Guide.pdf" > VIVO Release 1
v1.2 Installation Guide< / a >
on "Using an External Authentication System
with VIVO".
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< / li >
< / ul >
< / blockquote >
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< p >
4. If you had modified < code > web.xml< / code >
to configure the Pellet Reasoner (as described
in the installation instructions), repeat that modification.
< / p >
< p >
5. Stop Apache Tomcat and run ant by typing: < code > ant all< / code >
< / p >
< p >
6. Start Apache Tomcat and log in to VIVO.
< / p >
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< h3 id = "ontology" > IV. Ontology Changes< / h3 >
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< h4 id = "verify_ontology_upgrade" > i. Verify Ontology upgrade process< / h4 >
< p >
After Apache Tomcat is started, these files should be reviewed to
verify that the automated upgrade process was executed
successfully. The ontology alignment process will create the
following files in the Tomcat < code > webapps/vivo/WEB-INF directory< / code > :
< / p >
< dl >
< dt >
< code > ontologies/update/logs/knowledgeBaseUpdate.log< / code >
< / dt >
< dd >
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A log of a summary of updates that were made to the knowledge base and
notes about some recommended manual reviews. This file should end with
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"Finished knowledge base migration".
If this file contains any warnings they should be reviewed with
your implementation team representative to see whether any
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corrective action needs to be taken.
< / dd >
< / dl >
< dl >
< dt >
< code > ontologies/update/logs/knowledgeBaseUpdate.error.log< / code >
< / dt >
< dd >
A log of errors that were encountered during the upgrade process. This
file should be empty if the upgrade was successful.
< / dd >
< / dl >
< dl >
< dt >
< code > ontologies/update/changedData/removedData.n3< / code >
< / dt >
< dd >
An N3 file containing all the statements that were removed from the
knowledge base.
< / dd >
< / dl >
< dl >
< dt >
< code > ontologies/update/changedData/addedData.n3< / code >
< / dt >
< dd >
An N3 file containing all the statements that were added to the
knowledge base.
< / dd >
< / dl >
< h4 id = "ontology_knowledge_base" > ii. Ontology knowledge base manual review< / h4 >
< p >
Changes to the VIVO core ontology may require corresponding
modifications of the knowledge base instance data and local ontology
extensions.
< / 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 following
types of changes:
< / p >
< dl >
< dt >
Class or Property renaming
< / dt >
< dd >
All references to the class (in the subject or object position) will be
updated to the new name. References to the property will be updated to
the new name.
< / dd >
< / dl >
< dl >
< dt >
Class or Property deletion
< / dt >
< dd >
All individuals in a deleted class will be removed.
< br >
All statements using a deleted property will be changed to use the
nearest available superproperty. If there is no available superproperty
then the statement will be deleted from the knowledge base. Note that
all removed and added data is recorded in the files in the changedData
directory.
< / dd >
< / dl >
< dl >
< dt >
Property addition
< / dt >
< dd >
If a newly added property is the inverse of a previously existing
property, the inverse of any statements using the pre-existing property
will be asserted.
< / dd >
< / dl >
< dl >
< dt >
Annotation property default values
< / dt >
< dd >
If a site has modified the value of a vitro annotation (such as
displayRankAnnot or displayLimitAnnot) so that it is no longer using
the default, then that setting will be left unchanged.
< br >
If a site is using the default value of a vitro annotation, and the
default has been changed in the new version of the ontology, then the
new default value will be propagated to the knowledge base.
< / dd >
< / dl >
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< h3 id = "fileSystem" > V. File Storage System Upgrade< / h3 >
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< h4 id = "changes_to_storage" > i. Changes to the File Storage System< / h4 >
< p >
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Each uploaded file exists as an individual in VIVO. When the browser
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requests an uploaded file from VIVO, the data model is queried to find
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out where the file is actually stored, so it can be downloaded to the
browser.
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< / p >
< p >
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In VIVO 1.2 this storage location, known as the "Alias URL" for
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the uploaded file, is stored in the file individual. That way, pages that
contain many files can be displayed much more quickly.
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< / p >
< p >
When Apache Tomcat starts up after the upgrade,
it will initiate a process to calculate the "Alias URL"
for each existing file and store it in the data model for fast access.
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< / p >
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< h4 id = "verify_file_upgrade" > ii. Verify File Storage System upgrade process< / h4 >
< p >
The File Storage upgrade process will create a log file in the
VIVO upload directory. You should review this file to ensure that
this upgrade worked properly.
< / p >
< dl >
< dt >
< code > upgrade/FileStorageAliasAdder-log.2011-00-00T00-00-00.txt< / code >
< / dt >
< dd >
A log of the upgrade process. The actual filename includes a timestamp
that tells when the upgrade executed.
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This file should end with< code > Finished adding alias URLs to FileByteStreams.< / code >
If this file contains any warnings they should be reviewed with
your implementation team representative to see whether any
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corrective action needs to be taken.
< / dd >
< / dl >
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< h3 id = "theme" > VI. Theme Changes< / h3 >
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< h4 id = "#newTheme" > Introducing a New Default Theme< / h4 >
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< p >
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VIVO 1.2 includes a new default theme called < strong > wilma< / strong >
(located in
/vivo/themes/wilma) which fully supports all 1.2 features. For details on how to
create your own theme using wilma as a starting point, please review the < a href = "http://www.vivoweb.org/support/user-guide/administration" title = "Download VIVO documentation" target = "_blank" > Site Administrator's Guide< / a > .
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< / p >
< blockquote id = "vivoBasicDeprecated" >
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< h4 > The vivo-basic theme has been deprecated with the 1.2 release and is not
recommended for production instances.< / h4 >
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< p >
Since vivo-basic was the default theme for all previous releases, it is
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included as part of VIVO 1.2 to help with the transition of upgrading
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existing installations to the latest code, but all vivo-basic development
has ceased and it will not be distributed in future releases.
< / p >
< p >
Please note that vivo-basic does not support all of the new 1.2 features.
Most notably, in choosing to use vivo-basic you will be missing out on the
following:
< / p >
< ul >
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< li >
new primary menu for site navigation (replaces tabs)
< / li >
< li >
home page with class group browse and visual graph
< / li >
< li >
menu pages with class group and individual browse
< / li >
2011-02-10 14:19:58 +00:00
< / ul >
< / blockquote >
< h4 id = "templateTransition" > Templates< / h4 >
< p >
The 1.2 release continues the transition from JavaServer Pages (.jsp) to
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Freemarker templates (.ftl) for generating web pages. While there are still
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JSP files in action behind the scenes, as of 1.2 all theme templates
are of the Freemarker variety and are located in the "templates" directory
within a theme.
< / p >
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< p >
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If you did not create a custom theme for your site previously, but used
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the vivo-basic theme in its original directory, you need not take any
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action in order to remain using the vivo-basic theme in 1.2.
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< / p >
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< p >
If you did make changes to the vivo-basic theme, you will need to reapply those changes.
We recommend you apply these changes to the wilma theme.
< / p >
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< blockquote >
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< strong > Please note:< / strong >
The vivo-basic theme has been deprecated and is < a href = "#vivoBasicDeprecated" > not recommended for production instances< / a > .
2011-02-10 14:19:58 +00:00
< / blockquote >
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< p >
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For details on the new structure of themes in 1.2 and further information
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regarding the development of your own custom theme, please review the < a href = "http://www.vivoweb.org/support/user-guide/administration" title = "Download VIVO documentation" target = "_blank" > Site Administrator's Guide< / a > . This document will focus on updating an existing
2011-02-10 14:47:05 +00:00
pre 1.2 theme.
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< / p >
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< h3 id = "setup_sdb" > VII. Set Up SDB Store in the Background (Optional)< / h3 >
< p >
If your VIVO installation is running in RDB mode, and you'd like to convert
to SDB, 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. Note that it
is important not to edit any data anywhere in the application while this
background conversion is running.
< / p >
< p >
To start the SDB conversion, log in as a system
administrator and request /sdbsetup (For example, if your VIVO is installed
at http://vivo.myuniversity.edu/ you would type
http://vivo.myuniversity.edu/sdbsetup into your browser).
< / p >
< p >
Click the button that appears on this page.
< / p >
< p >
During the course of the SDB setup, which may take several hours 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 store.
< / p >
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< / div >
<!-- end of content -->
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< div id = "footer" role = "contentinfo" >
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< p class = "copyright" >
< small >
© 2011
All Rights Reserved | < a class = "terms" href = "/termsOfUse" > Terms of Use< / a >
< / small >
| Powered by < a class = "powered-by-vivo" href = "http://vivoweb.org" target = "_blank" > < strong > VIVO< / strong > < / a >
< / p >
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< div id = "nav" role = "navigation" >
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< ul id = "footer-nav" role = "list" >
< li role = "listitem" >
< a href = "http://vivoweb.org/about" > About< / a >
< / li >
< li role = "listitem" >
< a href = "http://vivoweb.org/contact" > Contact Us< / a >
< / li >
< li role = "listitem" >
< a href = "http://www.vivoweb.org/support" target = "blank" > Support< / a >
< / li >
< / ul >
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< / div >
2011-02-09 23:36:30 +00:00
< / div >
2011-01-17 01:49:25 +00:00
< / body >
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< / html >
