VIVO Release 1 V1.4 Upgrade GuideDecember 9, 2011 - Upgrading from Release 1 V1.3 to Release 1 V1.4
If you need to do a fresh install, please consult the VIVO Release V1.4 Installation
Guide found on vivoweb.org
or the install.html file located in the
directory of the VIVO source code distribution. The installation document also has a
list of the required software and versions (there are no new hardware
or software requirements for V1.4).
For a description of the release contents see the Release announcement for V1.4.
Table of Contents
I. Before Performing the Upgrade
Create backups of:
- The VIVO distribution directory (which contains the source for VIVO 1.3)
- The VIVO home directory (pointed to by your deploy.properties file)
- The webapps directory in Tomcat
- MySQL database (most people use mysqldump to create the backup)
The upgrade process is similar to the initial install process with the following exceptions:
- You do not need to reinstall MySQL or recreate the MySQL database. Please backup your MySQL database as noted above.
- First-time login of the root 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.)
- The first time Apache Tomcat starts up after the upgrade, an automated process will modify the knowledge base to align the data with any ontology updates made for the new release. See the section on the Knowledge Base Migration below for more information.
II. Noteworthy Changes
New property in deploy.properties
proxy.eligibleTypeListdescribes which classes of Individuals are eligible for "self-editing" by proxy. See the table in Section III for more details.
Change to Tomcat configuration
In order for VIVO to correctly handle international characters, you must configure Tomcat to conform to the URI standard by accepting percent-encoded UTF-8.
Edit Tomcat's conf/server.xml and add the following attribute to each of the Connector elements: URIEncoding="UTF-8".
<Server ...> <Service ...> <Connector ... URIEncoding="UTF-8"/> ... </Connector> </Service> </Server>
III. Upgrade Instructions
1. Download the new distribution file and unpack it into a new source directory.
2. Create a new deploy.properties using the same settings 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,
|Property Name||Example Value|
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 a
certain structure and begin with the public web address of the VIVO
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
* The namespace must end with "individual/" (including the trailing slash).
|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).|
|Directory where tomcat is installed.|
|Name of your VIVO application.|
URL of Solr context used in local VIVO search.
Should consist of:
scheme + servername + port + vivo_webapp_name + "solr"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"
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.
|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.|
|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.|
|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 their accounts.|
|Specify the JDBC URL of your database. Change the end of the URL to reflect your database name (if it is not "vivo").|
|Change the username to match the authorized user you created in MySQL.|
|Change the password to match the password you created in MySQL.|
|Specify the maximum number of active connections in the database connection pool to support the anticipated number of concurrent page requests.|
|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.|
|Change the dbtype setting to use a database other than MySQL. Otherwise, leave this value unchanged. Possible values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and SQLServer. Refer to http://openjena.org/wiki/SDB/Databases_Supported for additional information.|
|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.|
|Change the validation query used to test database connections only if necessary to use a database other than MySQL. Otherwise, leave this value unchanged.|
Specify the email address of the root user
account for the VIVO application. This user will have an initial
temporary password of 'rootPassword'. You will be prompted to create a
new password on first login.
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.
|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 (the value of the property must be either a String literal or an untyped literal).|
|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.|
Log in using BearCat Shibboleth
The temporal graph visualization can require
extensive machine resources. This can have a particularly noticable
impact on memory usage if
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:
|An absolute file path, pointing to the root directory of the Harvester utility. You must include the final slash.|
|Types of individual for which we can create proxy editors. If this is omitted, defaults to http://www.w3.org/2002/07/owl#Thing|
3. Apply any previous changes you have made to the new source directory.
Special notes regarding source files
- 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.
- 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.
- NIH-funded VIVO implementations will need to apply the Google Analytics Tracking Code (GATC) to
googleAnalytics.ftlin the theme:[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftlA sample
googleAnalytics.ftlis 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, see the VIVO Google Analytics wiki page.
5. Stop Apache Tomcat and from your VIVO source directory, run
6. Start Apache Tomcat and log into VIVO as the root user when the upgrade is completed. Depending on the size of your database, the migration process may take up to several hours. When it is complete, you will see a message in the catalina.log file that the server has started.
INFO: Server startup in XXXXX ms
7. As root or an administrator, request a rebuild of the Solr search index: Go to the "Site Admin" page and click on "Rebuild Search Index" under the heading "Refresh Content".
8. Review and save aside the knowledge base migration logs.
The knowledge base migration process described in the next section will generate logs.
These logs will be overwritten if you redeploy the VIVO application (but not if you restart tomcat), and since
they may be a useful reference if questions come up about your 1.4 VIVO data after deployment, you should save them aside.
The logs are created in the Tomcat
- A log of a summary of updates that were made to the knowledge base. This file should end with "Finished knowledge base migration". If this file contains any warnings they should be reviewed with your implementation team representative to see whether any corrective action needs to be taken.
- A log of errors that were encountered during the upgrade process. This file should be empty if the upgrade was successful. If any errors are encountered you will need to rerun the knowledge base migration.
IV. Knowledge Base Migration
i.Knowledge Base Migration Process
For an description of changes to the VIVO ontology in version 1.4 see the sourceforge wiki page on ontology changes
Changes to the VIVO core ontology may require corresponding modifications to the knowledge base instance data and ontology annotations. When VIVO first starts up following the upgrade, it will initiate a process to examine the knowledge base and apply necessary changes. The knowledge base migration process will make the following types of changes:
- 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.
- Class or Property deletion
All type assertions of a deleted class will be removed.
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.
- Annotation property default values
If a site has modified the value of a vitro annotation (such
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 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.
- Structural changes
- Changes in the way individuals (intances of classes) are related to other individuals.
In addition to the logs described in step 8 of the previous section, the knowledge base migration process will log copies of all additions and deletions that were made to the knowledge base in the following files:
- An N3 file containing all the statements that were removed from the knowledge base.
- An N3 file containing all the statements that were added to the knowledge base.
ii. Knowledge Base Manual Review for Local ExtensionsNot all of the modifications that may be required are automated. If you have local extensions to areas of the ontology that have changed, a manual review of the knowledge base is recommended after the automated upgrade process.
[vivo_source_dir]/vitro-core/webapp/web/templates/freemarker/body/termsOfUse.ftlBe 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.
Now that you have VIVO up and running, please refer to the Site Administrator's Guide for information about its operation.