Upgrading NIH VIVO
to Release 1.0
Steps to Upgrade from Release 1 Version 0.9 to Release 1 Version 1.0
provides a short description of the steps involved in upgrading
your installation of NIH VIVO from Release 1 Version 0.9 to Release 1 Ve
This and other documentation
can be found at:
Table of Contents
Upgrading NIH VIVO to Release 1.0
I. Before Performing
II. The Upgrade Process
III. Ontology Changes
IV. Special Note re: Default Namespace
Before Performing the Up
Please read the bullet points below BEFORE beginning the upgrade.
The upgrade process is similar to the original ins
tall process with the
DO NOT reinstall MySQL or recreate the MySQL database. Please
the MySQL database.
It is not necessary to add RDF data or reconfigure the Apache HTTP
time login of the administrator account will use the password
previously set, NOT the password in deploy.properties.
Any image files that have been upl
oaded into the system will not be
disturbed by the upgrade.
he first time Apache Tomcat starts up after the upgrade, it will initiate
a process that modifies the knowledge base to align the data with the
revised ontology. See the section on "Ontology Chan
Ensure that backups are created of the Tomcat webapps directory, the
original source directory, and the MySQL database.
Download the new distribution file and unpack it into a new source
, using the same values as in your original
installation. Be aware that
now requires an
vitro.core.dir = ./vitro
The file example.deploy.properties
has been modified to show this.
any changes you have made to the new source directory.
: 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.
: At a minimum it will be necessary to apply the Google Analytics
Tracking code to footer.jsp in the theme:
For additional information and
a copy your institution's tracking code, see the
Google Analytics wiki page.
: Version 1 Release 0.9 contained two directories called "modifications"
and "ontology". These directori
es have been combined into a directory called
"productMods". If your site has made changes to the ontology ensure that
those changes are moved into the appropriate subdirectory of
This process assumes any changes made to the applicati
in the source directory and deployed, and
not made directly within
If you had modified
configure the Pellet Reasoner
in the installation instructions), repeat that modification.
ache Tomcat and r
un ant deploy by typing: ant
If you have setup the Apache Tomcat Connector using mod_jk and
modified your tomcat/conf/server.xml file, you will need to add 4 lines
to your context section, see examples below.
Context section befor
Context section after:
t type="java.lang.String" override="false"
Also, if you have these 3 lines in your Apache virtual host
please remove them!
y from all
Start Apache Tomcat
and login to VIVO.
Rebuild the Lucene search index as described in step IX of
process. This step will ensure that changes in the RDFdata to align
with the latest version of the core ontology
will be re
flected in the
Changes to the VIVO core ont
ology may require corresponding
of the knowledge base instance data and local ontology
When Apache Tomcat starts up following
the upgrade, it will
process to examine the knowledge base and apply necessary changes.
all of the modifications that may be required can be automated,
review of the knowledge base is recommended after the
process. The automated proc
ess will make only the following types of
Class or Property renaming
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.
lass or Property deletion
All individuals in a deleted class will be changed to
the nearest available superclass (which may be owl:Thing).
All statements using a deleted property will be changed
to use the nearest available su
perproperty. 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.
Class or Property addition
a newly added class has a superclass and there are
individuals in that superclass, then a note will be
added to the log file suggesting review of those individuals to
see if they should be reasserted in the newly added class.
If a newly
added property has a superproperty and there are
statements using the superproperty, then a note will be added to
the log file suggesting review of those statements to see if they
should be reasserted using the newly added property.
ion property default values
It 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.
If a site is using the d
efault 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.
The ontology alignment process will create the following files in the
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
"Successfully finished pr
ocessing ontology changes".
a log of errors that were encountered during the upgrade process. This file
should be empty if the upgrade was successful.
a file containing all the statements that were removed from the knowledge
a file containing all the statements that w
ere added to the knowledge base.
After Apache Tomcat is started, these files shou
ld be reviewed to verify that
the automated upgrade process was executed successfully.
IV. Special Note re: Default Namespace
recommend changing the default namespace after you have
populated your VIVO knowledge base, since there is currently no
migrate existing data to reflect the new namespace. Note that your VIVO
installation will not support linked data access methods unless the
namespace corresponds to the base URL of your site, as outlined in section
IV of the VIVO installation doc
ument, so if you set up an additional server,
such as a test server, using your production data, the linked data
functionality will not work. If you have questions about your current
namespace setting or need to change it, please contact the VIVO team at