Deprecated. This material represents early efforts and may be of interest to historians. It doe not describe current VIVO efforts.
Deprecated. This material represents early efforts and may be of interest to historians. It doe not describe current VIVO efforts.
This document contains instructions on how to upgrade your installation of VIVO from Version 1.5 (or 1.5.1) to Version 1.6. This and other documentation can be found on the support page at VIVOweb.org
If you need to do a fresh install, please consult the VIVO Release V1.6 Installation Guide found on vivoweb.org or the install.html file located in the doc
directory of the VIVO source code distribution. The installation document also has a list of the required software and versions.
For a description of the release contents see the Release announcement for V1.6.
If you have used temporary models in the database to stage ingested data, you will want to clear out any unneeded models that remain listed on the Manage Jena Models page (under "Ingest tools"). This step is especially important if these temporary models contain blank nodes, as this may cause unwanted or duplicate data to appear following the upgrade.
The upgrade process is similar to the initial install process with the following exceptions:
The VIVO build script now includes a distribute
target that will produce a file called distribution.tar.gz
. This compressed archive contains these files:
vivo.war
-- a WAR file for the main VIVO application.vivosolr.war
-- a WAR file for the Solr application.solrhome.tar
-- a Solr home directory that is configured for use with VIVO.To permit this portability, the deploy.properties
file has been split in two. build.properties
contains only the properties that are required for building VIVO. runtime.properties
, which must be created in the Vitro home directory, contains the properties that VIVO uses while running.
If you are building to deploy
to Tomcat (as with previous releases), then build.properties
must contain these properties:
vitro.core.dir
webapp.name
tomcat.home
vitro.home
-- note that this was vitro.home.directory
in previous releasesIf you are building to distribute
, the build.properties
file requires only these properties:
vitro.core.dir
webapp.name
In previous releases, Solr was deployed to Tomcat with a RemoteAddrValve
that would only permit access from certain IP addresses. Acceptable IP addresses were those which matched the regular expression pattern in the vitro.local.solr.ipaddress.mask
property.
This has been removed because:
Sites that need to secure Solr are now left to their own devices.
In previous releases, the properties file for the VIVO logging system was called default.log4j.properties
. In release 1.6, this file has been renamed to log4j.properties
. This is so the developers and implementers will know where to look for the file.
Note that debug.log4j.properties
, if present, will still override the default.
With release 1.6, the property group menu bar that was used on profile pages has been replaced by java script enabled tabs. When clicked, each property group tab will display the properties within that group while the contents of the previously displayed group will be hidden. The array of tabs also includes a "View All" tab that, when clicked, displays the contents of all the property groups.
The VIVO software now supports the development of SPARQL query data getters that can be associated with specific ontological classes. These data getters, in turn, can be accessed within Freemarker templates to provide richer content on VIVO profile pages. For example, the profile page for an academic department lists only the names of the faculty within that department and their titles, but with a SPARQL query data getter it is now possible to extend the faculty information to display all of the faculty members' research areas. Refer to this wiki page for details on how to use class-specific SPARQL query data getters: https://wiki.duraspace.org/display/VIVO/Enriching+VIVO+Content+Using+SPARQL+Query+Data+Getters
.
The template individual--foaf-person.ftl has been moved to the "templates" subdirectory in the wilma theme directory (vivo/themes/wilma/templates). If your installation has a customized version of individual--foaf-person.ftl, ensure that it is located in the templates subdirectory in your installation's theme directory or, if your installation does not have it's own theme directory, in the themes/wilma/templates subdirectory
.
VIVO now supports multiple profile pages for foaf:Persons. This feature, which is optional so installations can continue to use just the individual--foaf-person.ftl template, currently consists of two profile page types: a standard view, which is a redesigned version of the foaf:Person template in previous releases; and a quick view, which emphasizes the individual's own web page presence while providing summary VIVO information, such as current positions and research areas. The profile quick view requires the use of a web service that captures images of web pages. This web service is not included with the VIVO software. An installation will either have to develop their own service or use a third-party service, usually for a small fee depending on the number of images served. (Examples of these services include WebShotsPro, Thumbalizr and Websnapr.) For more information on how to implement multiple profile page views, refer to this wiki page: https://wiki.duraspace.org/display/VIVO/Multiple+foaf%3APerson+Profile+Pages
.
For Release 1.6 the VIVO Home Page has been redesigned. The Search field beneath the "welcome" text now allows the user to limit the results of a search to a specific class group, such as people, organizations, etc. In addition, the browse-by-class-group display has been removed from the Home Page and replaced by multiple features, which include: a list of four randomly selected faculty members, including their titles and thumbnail images; a display of statistical data about the VIVO installation, such as the number of people, activities and organizations; and, optionally a global map showing researchers' areas of geographic focus.
The RDF files that initialize the data model have moved, in both the distribution and the runtime locations. In the distribution, they have been collected in one place, and reorganized to use a more consistent naming scheme. During the build process, they are copied to a location within the VIVO home directory, instead of residing in the webapp itself.
If you have modified these RDF files, or added files of your own, you must adjust to the new locations accordingly.
Old locations of RDF files under [Vitro]/webapp/web or [VIVO]/productMods | New locations of RDF files under [Vitro]/webapp/rdf or [VIVO]/rdf | Comments |
---|---|---|
WEB-INF/ontologies/app/ | rdf/display/firsttime/ | |
WEB-INF/ontologies/app/loadedAtStartup/ | rdf/display/everytime/ | |
WEB-INF/ontologies/app/menuload/displayTBOX.n3 | rdf/displayTbox/everytime/ | Was one file, now a directory |
/WEB-INF/ontologies/app/menuload/displayDisplay.n3 | rdf/displayDisplay/everytime/ | Was one file, now a directory |
WEB-INF/ontologies/user/applicationMetadata/ WEB-INF/init-data/ | rdf/applicationMetadata/firsttime/ | Merged directories |
WEB-INF/ontologies/user/abox/ | rdf/abox/firsttime/ | |
WEB-INF/filegraph/abox/ | rdf/abox/filegraph/ | |
WEB-INF/ontologies/user/tbox/ | rdf/tbox/firsttime/ | |
WEB-INF/filegraph/tbox/ | rdf/tbox/filegraph/ |
If you are using a three-tier build process, you will need to add two lines to the build script to accomodate the RDF files, and the language support (see below) So this:
<patternset id="appbase.patterns"> <include name="src/**/*" /> <include name="lib/**/*" /> <include name="test/**/*" /> <include name="themes/**/*" /> <include name="config/*.properties" /> <include name="config/*.txt" /> <include name="config/jarlist/*.txt" /> <include name="config/solr/*" /> <include name="context.xml" /> </patternset>becomes this:
<patternset id="appbase.patterns"> <include name="src/**/*" /> <include name="lib/**/*" /> <include name="rdf/**/*" /> <include name="languages/**/*" /> <include name="test/**/*" /> <include name="themes/**/*" /> <include name="config/*.properties" /> <include name="config/*.txt" /> <include name="config/jarlist/*.txt" /> <include name="config/solr/*" /> <include name="context.xml" /> </patternset>
VIVO 1.6 includes limited support for other languages, in addition to American English. This limited support is described as read-only support on public-facing pages.
Read-only means that there is no provision for editing multi-language data or displays. Property values, ontology labels, etc. must all be provided in RDF files and ingested or otherwise inserted into the data model. The Page Management user interface does not support maintaining pages in multiple languages.
Public-facing means that most of the pages used for site adminstration are only presented in American English.
These two pages in the VIVO Wiki describe how to Build VIVO with multiple languages and how to Add a new language to VIVO.
In VIVO 1.6, the response to requests for linked data is changed, to be smaller and faster.
When responding to a request for linked data about an individual, VIVO 1.6 returns:
VIVO releases prior to VIVO 1.6 returned a more complex set of statements, referred to as "extended linked data":
Extended linked data was costly to produce, in terms of resources, because it required a recursive search of the data model. Extended linked data typically contained 50% more information than its non-extended equivalent, and took more than 10 times as long to produce.
VIVO release 1.6 can be configured to produce extended linked data like previous releases. However, extended linked data will not be supported in future releases.
The list of default types for Google Refine has changed, to accomodate changes in the ontology. If you are using Google Refine, you may need to change your runtime properties accordingly. The new defaults appear in example.runtime.properties
.
This release includes several settings to help developers by instumenting the freemarker templates and the SPARQL queries on the RDFService. Check the wiki for details, or look in the home directory in example.developer.properties
.
For this release, the following browsers are supported.
1. Download the new distribution file and unpack it into a new source directory.
2. Separate your existing deploy.properties
file into two files, as described below. Store the new build.properties
file in the top level of the VIVO distribution directory. Store the new runtime.properties
file in your VIVO home directory.
Properties in build.properties | Properties in runtime.properties |
---|---|
vitro.core.dir vitro.home tomcat.home webapp.name | All other properties from deploy.properties |
Note that vitro.home replaces vitro.home.directory Note that vitro.local.solr.ipaddress.mask is no longer used. |
If you prefer, you may start with example.build.properties
and example.runtime.properties
, make copies, and edit them to suit your installation. Remember, the runtime.properties
file goes into your VIVO home directory.
The properties below are new to build.properties
. They are optional, so you need not add them unless you want a value other than the default.
Property Name | Example Value |
---|---|
Languages (in addition to American English) that will be built into your VIVO site. The languages must be found in the languages directory of the VIVO distribution. See the VIVO Wiki for more information. | |
languages.addToBuild | es_MX |
The properties below are new to runtime.properties
. They are optional, so you need not add them, unless you want a value other than the default.
Property Name | Example Value |
---|---|
Tell VIVO to generate HTTP headers on its responses to facilitate caching the profile pages that it creates. This can improve performance, but it can also result in serving stale data. Default is false if not set. For more information, see the VIVO wiki page: Use HTTP caching to improve performance | |
http.createCacheHeaders | true |
Force VIVO to use a specific language or Locale instead of those specified by the browser. This affects RDF data retrieved from the model, if RDFService.languageFilter is true. This also affects the text of pages that have been modified to support multiple languages. | |
languages.forceLocale | en_US |
A list of supported languages or Locales that the user may choose to use instead of the one specified by the browser. Selection images must be available in the i18n/images directory of the theme. This affects RDF data retrieved from the model, if RDFService.languageFilter is true. This also affects the text of pages that have been modified to support multiple languages. | |
languages.selectableLocales | en, es, fr_FR |
On the VIVO home page, display a global map highlighting the geographical focus of foaf:person individuals. The default is enabled . | |
homePage.geoFocusMaps | enabled |
MultiViews for foaf:person profile pages. VIVO supports the simultaneous use of a full foaf:Person profile page view and a "quick" page view that emphasizes the individual's own webpage presence. Implementing this feature requires an installation to develop a web service that captures images of web pages or to use an existing service outside of VIVO, usually for a small fee. The default is disabled . | |
MultiViews.profilePageTypes | disabled |
Setting this property causes VIVO 1.6 to produce extended responses to requests for linked data. This provides compatibility with earlier releases. The default is false . Extended linked data is costly, in terms of server resource. Typically, extended linke data contains 50% more information than its non-extended equivalent, and takes 10 times as long to produce. Extended linked data will not be supported in future releases of VIVO. | |
serveExtendedLinkedData | true |
Note that the property named externalAuth.buttonText
is no longer used. You can specify the text of the external login button by adding a property to all.properties
like this:
external_login_text = Log in using BearCat Shibboleth
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.ftl
in the theme:[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftlA samplegoogleAnalytics.ftl
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, see the VIVO Google Analytics wiki page.
4. Apply any previous changes you have made to the RDF initialization files. See the section on the Auto-loaded RDF files above for more details.
5. Stop Apache Tomcat and from your VIVO source directory, run ant by typing: ant all
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 the knowledge base migration logs. The knowledge base migration process described in the next section will create logs in a subdirectory of the VIVO home directory:
(home directory)/update/logs/knowledgeBaseUpdate.(timestamp).log 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.
ontologies/update/logs/knowledgeBaseUpdate.(timestamp).error.log 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.
9. Load the About Page .N3 file (optional). Release 1.6 provides an "about VIVO" page that is editable through the GUI, using the Page Management functionality. If your installation has a customized version of the About Page and you do not need to have it accessible via Page Management, then skip this step. Otherwise, here are the instructions for loading the About Page .N3 file:
productMods/WEB-INF/ontologies/app/aboutPage.n3
.If your installation has a customized version of the About Page, but you would like to make its content editable through the GUI, follow the above steps and then use Page Management to update the fixed HTML content.
Changes to the VIVO core ontology may require corresponding modifications to the knowledge base instance data and ontology annotations. The first time VIVO starts up following the upgrade, it will initiate a process to examine the knowledge base and apply necessary changes. The knowledge base migration process for release 1.6 will make the following types of changes:
Instance data changes to align with VIVO-ISF Obsolete predicates and types in the instance data will be updated where necesary to correspond to the current properties and classes in version 1.6 of the VIVO-ISF ontology. Note that VIVO 1.6 continues to make use of certain deprecated classes and properties that are not incompatible with VIVO-ISF. Most notable among these are the various subclasses of foaf:Person: these types will be unchanged by the VIVO 1.6 data migration, but may be removed in a future release.
Annotation property default values 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. Note that the annotation settings for certain obsolete VIVO 1.5 properties will be preserved in a configuration file that applies settings to particular object properties based on the types of their subject and object individuals. This file is found in the VIVO home directory: (home directory)/rdf/display/everytime/PropertyConfig.n3 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.
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 in the VIVO home directory:
(home directory)/upgrade/knowledgeBase/changedData/removedData.(timestamp).n3 An N3 file containing all the statements that were removed from the knowledge base.
webapps/vivo/WEB-INF/ontologies/update/changedData/addedData.(timestamp).n3 An N3 file containing all the statements that were added to the knowledge base.
VIVO comes with a "Terms of Use" statement linked from the footer. The "Site Name" you assign in the "Site Information" form under the Site Admin 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:
[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.
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