VIVO Release 1 V1.3 Installation Guide

Release anouncement for V1.3

Search

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.

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.

Authorization

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.

Menu management

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.

FreeMaker template improvements

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.

Visualization

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.

Several visualization also now provide a caching feature that improves performance after the initial processing.

QR Codes

Pages for people in VIVO now have an icon for displaying QR codes to allow capturing names and available contact information on mobile devices.

Harvester Integration

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.

Ontology changes

• support for certifications and licenses
• expanded support for intellectual property (patents) (it was there as stub before but didn't allow common things such as assignee and issuer)
• support for editorial, reviewing and organizing activities
• expanded shared geographical instance data vocabulary to include the 50 U.S. states
• representing specific types of EducationalTraining: PostdoctoralTraining, Internship, MedicalResidency

Linked open data

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.

Installation process for V1.3

This document is a summary of the VIVO installation process. This and other documentation can be found on the support page at VIVOweb.org

• 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 over an existing installation of an earlier version.
• If you are going to upgrade an existing service, please consult the "upgrade" files in this directory.

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.

Where does VIVO live on your computer?

Before beginning the installation, let's look at the four locations on your computer that will hold VIVO.

The VIVO distribution directory

This is created when you unpack the VIVO distribution file (see Step III, below). This is where you will create your deploy.properties file (see Step V, below), and where you will make any modifications to the VIVO theme or code. You can create this wherever you choose.

VIVO inside Tomcat

When you run the build script to compile and deploy VIVO (see Step VI, 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 script again. Tell the build script where to find Tomcat by setting tomcat.home in the deploy.properties file (see Step V, below).

The VIVO home directory

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 vitro.home.directory in the deploy.properties file (see Step V, 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.

The MySQL database

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 Step I, below). but you won’t need to know the location. You will access the data through VIVO, or occasionally through the MySQL client application.

I. Install required software

Before installing VIVO, make sure that the following software is installed on the desired machine:

• Java (SE) 1.6 or higher, http://java.sun.com (Not OpenJDK)
• Apache Tomcat 6.x, http://tomcat.apache.org
• Apache Ant 1.7 or higher, http://ant.apache.org
• MySQL 5.1 or higher*, http://www.mysql.com

Be sure to set up the environment variables for JAVA_HOME and ANT_HOME and add the executables to your path per your operating system and installation directions from the software support websites.

* 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.

* Note that VIVO is not yet compatible with Tomcat 7.

II. Create an empty MySQL database

Decide on a database name, username, and password. Log into your MySQL server and create a new database in MySQL that uses UTF-8 encoding. 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 dbname, username, and password. Most of the time, the hostname will equal localhost.

                CREATE DATABASE dbname CHARACTER SET utf8;

Grant access to a database user. For example:

                GRANT ALL ON dbname.* TO 'username'@'hostname' IDENTIFIED BY 'password';

Keep track of the database name, username, and password for Step IV.

III. Download the VIVO Application Source

Download the VIVO application source as either rel-1.3.zip or rel-1.3.gz file and unpack it on your web server:
http://vivoweb.org/download

IV. Specify deployment properties

At the top level of the VIVO distribution directory, copy the file example.deploy.properties to a file named simply deploy.properties. This file sets several properties used in compilation and deployment.

Windows: 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. c:/tomcat.

External authentication: 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 Using an External Authentication System with VIVO.

    scheme + servername + port + vivo_webapp_name + "solr"

V. Compile and deploy

At the command line, from the top level of the VIVO distribution directory, type:

                ant all
            

to build VIVO and deploy to Tomcat's webapps directory.

VI. Set Tomcat JVM parameters and security limits

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).

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. If this file does not exist in Tomcat's bin directory, you can create it.
For example:

                    export CATALINA_OPTS="-Xms2048m -Xmx1024m -XX:MaxPermSize=128m"
                

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 be sufficient.

If an OutOfMemoryError is encountered during VIVO execution, it can be remedied by increasing the heap parameters and restarting Tomcat.

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 /etc/security/limits.conf:

                    apache	hard	nproc	400
                    tomcat6	hard	nproc	1500 
                

VII. Start Tomcat

Most Tomcat installations can be started by running startup.sh or startup.bat 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 in catalina.out or localhost.log

VIII. Log in and add RDF data

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 rootUser.emailAddress 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 functionality throughout the site.

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 ontology, but you may also upload other ontologies from an RDF file.

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 likely want to check "create classgroups automatically."

Clicking the "Index" tab in the navigation bar at the top right of the page will show a simple index of the knowledge base.

See more documentation for configuring VIVO, ingesting data, and manually adding data at http://vivoweb.org/support.

IX. Set the Contact Email Address (if using "Contact Us" form)

If you have configured your application to use the "Contact Us" feature in Step IV (email.smtpHost), 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.

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 Email Address" and submit the change.

If you set the email.smtpHost in Step IV and do NOT provide an email address in this step, your users will receive a java error in the interface.

X. Set up Apache Tomcat Connector

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).

This will make VIVO available at "http://example.com" instead of "http://example.com:8080/vivo"

Using the mod_jk connector allows for communication between Tomcat and the primary web server. The Quick Start HowTo on the Apache site describes the minimum server configurations for several popular web servers.

After setting up the mod_jk connector above, you will need to modify the Tomcat's server.xml (located in [tomcat root]/conf/) to respond to requests from Apache via the connector. Look for the <connector> directive and add the following properties:

                connectionTimeout="20000" maxThreads="320" keepAliveTimeout="20000"  
            

Note: the value for maxThreads (320) is equal to the value for MaxClients in the apache's httpd.conf file.

Locate the <Host name="localhost"...> directive and update as follows:

              <Host name="localhost" appBase="webapps"
                       DeployOnStartup="false"
                       unpackWARs="true" autoDeploy="false"
                       xmlValidation="false" xmlNamespaceAware="false">
                   
                   <Alias>example.com</Alias>
                   
                   <Context path=""
                           docBase="/usr/local/tomcat/webapps/vivo"
                           reloadable="true"
                           cookies="true" >
                   
                       <Manager pathname="" />
                   
                       <Environment type="java.lang.String" override="false"
                               name="path.configuration"
                               value="deploy.properties"
                       />
                   </Context>
                  
                   ...
            

XI. Using an External Authentication System with VIVO

VIVO can be configured to work with an external authentication system like Shibboleth or CUWebAuth.

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.

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.

Configuring the Apache server

Your institution will provide you with instructions for setting up the external authentication system. The Apache server must be configured to secure a page in VIVO. When a user reaches this secured page, the Apache server will invoke the external authentication system.

For VIVO, this secured page is named: /loginExternalAuthReturn

When your instructions call for the location of the secured page, this is the value you should use.

Configuring VIVO

To enable external authentication, VIVO requires three values in the deploy.properties file.

• The name of the HTTP header that will hold the external user's network ID.

  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.

  You need to tell VIVO the name of that HTTP header. Insert a line like this in the deploy.properties file:

  externalAuth.netIdHeaderName = [the header name]

  For example:

  externalAuth.netIdHeaderName = remote_userID

• The text for the Login button.

  To start the authentication process, the user will click on a button in the VIVO login form. You need to tell VIVO what text should appear in that button.

  Put a line like this in the deploy.properties file: externalAuth.buttonText = [the text for your login button] For example:

  externalAuth.buttonText = Log in using BearCat Shibboleth

  The VIVO login form will display a button labelled "Log in using BearCat Shibboleth".

• Associating a User with a profile page.

  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 for matching. Insert a line like this in the deploy.properties file:

  selfEditing.idMatchingProperty = [the URI of the property]

  For example:

  selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId

XII. Was the installation successful?

If you have completed the previous steps, you have good indications that the installation was successful.

• Step VII showed that Tomcat recognized the webapp, and that the webapp was able to present the initial page.
• Step VIII verified that you can log in to the administrator account.

Here is a simple test to see whether the ontology files were loaded:

• Click on the "Index" link on the upper right, below the logo. 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 time that Tomcat was started.
• Click on the "Country" link. You should see an alphabetical list of the countries of the world.

Here is a test to see whether your system is configured to serve linked data:

• Point your browser to the home page of your website, and click the "Log in" link near the upper right corner. Log in with the rootUser.emailAddress you set up in Step IV. If this is your first time logging in, you will be prompted to change the password.
• 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.
• 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.
• Open a new web browser or browser tab to the page http://marbles.sourceforge.net/. In the pink box on that page enter the URI of the individual you created in the previous step and click "open."
• 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 serving linked data.

Finally, test the search index.

• 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 administrator and go to "http://your-vivo-url/SearchIndex".

XIII. Review the VIVO Terms of Use

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.ftl

Next Step ...

Now that you have VIVO up and running, please go read the Site Administrator's Guide.