Vitro Version 1.5. Installation Guide

This document is a summary of the Vitro installation process.

These instructions assume that you are performing a clean install, starting with an empty database, an empty Vitro home directory, and a Tomcat installation with no Vitro webapp. If you are upgrading a previous installation of Vitro, you may need to adjust your procedure accordingly.

Other servlet containers: If you want to use a servlet container other than Tomcat, please consult instructions for other servlet containers in this directory.

Introduction to the Vitro installation

Before beginning the installation, let’s discuss some of the major concepts relating to the Vitro installation.

Where does Vitro live on your computer?

Vitro exists in four locations on your computer, from the distribution to the runtime to the data storage.

The Vitro distribution directory

This is created when you checkout the Vitro source code (see installation step III, below). This is where you will create your build.properties file (see installation step IV, below), and where you will make any modifications to the Vitro theme or code. You can create this wherever you choose.

Vitro inside Tomcat

When you run the build script to compile and deploy Vitro (see installation step VI, below), the files will be deployed to a directory inside Tomcat. This is the actual executing code for Vitro, but you won’t need to look at it or change it. If you need to change Vitro, 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 build.properties file (see installation step IV, below).

The Vitro home directory

This directory contains the runtime configuration properties for Vitro. Vitro will also use this area to store some of the data it uses. Uploaded image files are stored here, and the Solr home directory is stored here also. You can create this wherever you choose. Tell Vitro where to find the home directory by setting vitro.home in the build.properties file (see installation step IV, below). You must create this directory before starting Vitro, you must create the runtime.properties file in this directory (see Step V, below), 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 Vitro 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 installation step I, below). but you won’t need to know the location. You will access the data through Vitro, or occasionally through the MySQL client application.

The relationship between Vitro and VIVO

“Vitro Inside”

Vitro was developed as a “general-purpose web-based ontology and instance editor with customizable public browsing.” It is useful on its own, but also serves as the basis for several products, including VIVO. [http://sourceforge.net/projects/vivo/]

In 2009, the National Institutes of Health (NIH) awarded a major grant to advance the development of VIVO. Much of the recent development on Vitro has been in support of that grant. However, Vitro retains its own identity, and still serves as the core of many projects and products. Some of these are currently in use, and some are still in the planning stages.

Because VIVO was so well funded, and because it is widely used, someone seeking help with Vitro might find information that applies to VIVO instead. In many cases, that information will apply to Vitro as well. However, there are some notable exceptions:

• Ontology

  Vitro is essentially a blank slate, and is suitable for use with almost any ontology. It is packaged with a minimal ontology, sufficient to run the application itself.

  VIVO is packaged with a rich ontology, tailored to scientists and educators.

• Theme

  Vitro and VIVO are each packaged with their own default theme. The VIVO theme is more extensive, since it includes custom pages and custom list views that apply to the VIVO ontology.

• Visualizations

  VIVO includes some rich visualization tools that are specific to the VIVO ontology.

• Harvester

  VIVO includes an RDF Harvester tool for importing data from sources of record. The Harvester may be useful for Vitro as well, but it was developed for VIVO, and may have some dependencies on VIVO.

Release schedule and names

Currently, the Vitro release schedule is coordinated with the VIVO releases, so version 1.4 of Vitro forms the basis of version 1.4 of VIVO. In the Vitro code repository, the release tags illustrate this relationship. For example, the Vitro revision that was tagged for version 1.4 of VIVO is named “rel-vivo-1.4”

Installation process for Version 1.4

This document is a summary of the Vitro installation process.

I. Install required software

Before installing Vitro, 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 or higher, http://tomcat.apache.org
• Apache Ant 1.8 or higher, http://ant.apache.org
• MySQL 5.1 or higher*, http://www.mysql.com
• Apache Subversion 1.6.x or higher*, http://subversion.apache.org/

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.

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. Check out the Vitro Source Code

Download the latest stable release of Vitro from SourceForge: go to

      http://sourceforge.net/projects/vivo/files/Vitro%20Application%20Source/

If you want the very latest Vitro source, you can use subversion to check it out from SourceForge:

         svn checkout svn://svn.code.sf.net/p/vivo/vitro/code/trunk [Vitro_distribution_dir]

IV. Specify build properties

In the webapp/config directory of the Vitro distribution, copy the file example.build.properties to a file named simply build.properties. Edit the file to suit your installation, as described in the following table.

These properties are used in compilation and deployment. They will be incorporated into Vitro when it is compiled in Step VI. If you want to change these properties at a later date, you will need to stop Tomcat, repeat Step VI, and restart Tomcat.

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.

V. Specify runtime properties

In Step IV, you defined the location of the Vitro home directory, by specifying vitro.home in the build.properties file. Create that directory now.

In the webapp/config subdirectory of the Vitro distribution, you will find a file called example.runtime.properties. Copy this to the Vitro home directory you have created, renaming the copy to runtime.properties. Edit the file to suit your installation, as described in the following table.

These properties are loaded when Vitro starts up. If you want to change these properties at a later date, you will need to restart Tomcat for them to take effect. You will not need to repeat Step VI.

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 Vitro.

    scheme + servername + port + vitro_webapp_name + "solr"

VI. Compile and deploy

At the command line, change to the webapp directory inside the Vitro distribution directory. Then type:

                ant all
            

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

VII. Configure Tomcat

Set JVM parameters

Vitro may 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="-Xms512m -Xmx512m -XX:MaxPermSize=128m"
                

This sets Tomcat to allocate an initial heap of 512 megabytes, a maximum heap of 512 megabytes, and a PermGen space of 128 megs. Lower values may suffice, especially for small test installations.

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

Set security limits

Vitro 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 
                

Set URI encoding

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>
            

Note: some versions of Tomcat already include this attribute as the default.

Take care when creating Context elements

Each of the webapps in the Vitro distribution (Vitro and Solr) includes a "context fragment" file, containing some of the deployment information for that webapp.

Tomcat allows you to override these context fragments by adding Context elements to "server.xml". If you decide to do this, be sure that your new Context element includes the necessary deployment parameters from the overridden context fragment.

See Section XI below, for an example of overriding the Vitro context fragment.

VIII. 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/vitro/" to test the application.

On start up Vitro will run some diagnostic tests. If a problem is detected, the normal Vitro pages will redirect to a startup status page describing the problem. You can stop tomcat, attempt to fix the problem and proceeded from Step VI. The startup status page may offer a continue link which will allow you to use VIVO in spite of the problems.

If Tomcat does not start up, or the Vitro application is not visible, check the files in Tomcat's logs directory. Error messages are commonly found in catalina.out or localhost.log

IX. Log in and add RDF data

If the startup was successful, you will see a welcome message informing you that you have successfully installed Vitro. 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. Vitro comes with a minimal ontology. You will likely want to upload additional 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.

X. 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 Vitro 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.

XI. 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. /vitro).

This will make Vitro available at "http://example.com" instead of "http://example.com:8080/vitro"

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/vitro"
                           reloadable="true"
                           cookies="true" >
                   
                       <Manager pathname="" />
                   </Context>
                  
                   ...
            

XII. Using an External Authentication System with Vitro

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

Vitro 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 Vitro, to identify the user.

If Vitro has an account for that user, the user will be logged in with the privileges of that account. In the absence of an account, Vitro 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 Vitro. When a user reaches this secured page, the Apache server will invoke the external authentication system.

For Vitro, 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 Vitro

To enable external authentication, Vitro requires three values in the runtime.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 Vitro the name of that HTTP header. Insert a line like this in the runtime.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 Vitro login form. You need to tell Vitro what text should appear in that button.

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

  externalAuth.buttonText = Log in using BearCat Shibboleth

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

• Associating a User with a profile page.

  Vitro will try to associate the user with a profile page, so the user may edit his own profile data. Vitro 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 Vitro what property should be used for matching. Insert a line like this in the runtime.properties file:

  selfEditing.idMatchingProperty = [the URI of the property]

  For example:

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

XIII. Was the installation successful?

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

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

Step VIII also shows that the Vitro self-tests ran successfully. When Tomcat starts the Vitro webapp, it runs several tests. If any of these tests produce warnings or error message, you would see them instead of the Vitro home page.

Among other things, the self-tests check

• The Vitro home directory exists and Vitro can write to it.
• Vitro can connect to the database.
• Vitro can connect to the Solr search application.

XIV. Review the Vitro Terms of Use

Vitro 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:

[vitro_source_dir]/webapp/web/templates/freemarker/body/termsOfUse.ftl

Next Steps

For more information about Vitro see the Vitro public website. In addition, you may find helpful information in the VIVO Site Administrator's Guide.

Send questions or comments to Vitro developers and designers at vivo-dev-all@lists.sourceforge.net.