vivo/doc/install.txt

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This document is a summary of the VIVO installation process. This and other documentation
can be found at:

     http://vivoweb.org/support
    
PLEASE NOTE!
These instructions assume that you are performing a clean install, 
including emptying an existing database 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.

Upgrade:
If you are going to upgrade an existing service, please consult the upgrade.txt
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.
 
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    * I. Install required software
    * II. Create an empty MySQL database
    * III. Download the VIVO Application Source
    * IV. Specify deployment properties
    * V. Compile and deploy
    * VI. Set Tomcat JVM parameters and security limits
    * VII. Start Tomcat
    * VIII. Log in and add RDF data
    * IX. Set the Contact Email Address (if using "Contact Us" form)
    * X. Setup Apache Tomcat Connector
    * XI. Configure Pellet Reasoner
    * XII. Using an External Authentication System with VIVO
    * XIII. Was the installation successful?

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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 or higher [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 setup 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 web sites.

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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.

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III. Download the VIVO Application Source

Download the VIVO application source as either rel-1.1.1.zip or rel-1.1.1.gz file 
and unpack it on your web server:
      
      http://vivoweb.org/download

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IV. Specify deployment properties

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

NOTE: 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".

                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 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 http://www.example.edu/vivo/individual/
                Note:  The namespace must end with "individual/" (including the 
                trailing slash).
property name:  Vitro.defaultNamespace 	
example value:  http://vivo.mydomain.edu/individual/

                Directory where Vitro code is located. In most deployments, 
                this is set to ./vitro-core, but it commonly points elsewhere 
                during development.
property name:  vitro.core.dir
example value:  ./vitro-core

                Directory where tomcat is installed
property name:  tomcat.home
example value:  /usr/local/tomcat

                Name of your VIVO application
property name:  webapp.name
example value:  vivo

                Directory where uploaded files will be stored. You must create 
                this directory ahead of time.
property name:  upload.directory
example value:  /usr/local/vivo/data/uploads

                Directory where the Lucene search index will be built. 	
                Depending on your permissions and who Tomcat is running as, 
                you may need to create this directory ahead of time.
property name:  LuceneSetup.indexDir 	
example value:  /usr/local/vivo/data/luceneIndex

                Specify an SMTP host that the form will use for sending 
                e-mail (Optional). If this is left blank, the contact form 
                will be hidden and disabled.
property name:  Vitro.smtpHost 	
example value:  smtp.servername.edu

                Specify the JDBC URL of your database.  Change the end of the
                URL to reflect your database name (if it is not "vivo").
property name:  VitroConnection.DataSource.url 	
example value:  jdbc:mysql://localhost/vivo

                Change the username to match the authorized user you created in MySQL
property name:  VitroConnection.DataSource.username
example value:  username

                Change the password to match the password you created in MySQL 	
property name:  VitroConnection.DataSource.password
example value:  password
	  	 
                Specify the name of your first admin user for the VIVO application. 
                This user will have an initial temporary password of 'defaultAdmin'. 
                You will be prompted to create a new password on first login.
property name:  initialAdminUser 	
example value:  defaultAdmin

                The name 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.
property name:  selfEditing.idMatchingProperty 	
example value:  http://vivo.mydomain.edu/ns#networkId

NOTE: 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".

                Temporal Graph Visualization is used to compare different 
                organizations/people within an organization on different parameters 
                like number of publications, grants. This parameter will be used 
                as a default in case a URI is not provided. It will be also used 
                whenever this visualization is to be rendered for top level organization.
                In absence of this parameter a SPARQL query will be fired which will 
                attempt to provide a top level organization.The name 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.
property name:  visualization.topLevelOrg
example value:  http://vivo-trunk.indiana.edu/individual/topLevelOrgURI

NOTE: 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".

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V. Compile and deploy

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

ant all

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

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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. 

For example: 

export CATALINA_OPTS="-Xms1024m -Xmx1024m -XX:MaxPermSize=64m"

This sets Tomcat to allocate an initial heap of 1024 megabytes, a maximum heap 
of 1024 megabytes, and a PermGen space of 64 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 

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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 
catalina.out file in Tomcat's logs directory. 

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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 initialAdminUser username you set up in 
Step IV. The initial password for initialAdminUser is defaultAdmin. On first 
login, you will be prompted to select a new password and verify it a second 
time.

After verifying your new password, 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 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 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 left 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.

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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 (Vitro.smtpHost), you will also need to add an email address to the VIVO 
application.  This is the email that the contact form submits to.  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 Vitro.smtpHost in Step IV and do NOT provide an email address
in this step, your users will receive a java error in the interface.

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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).

For example - 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 
http://tomcat.apache.org/connectors-doc/generic_howto/quick.html 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 ([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 
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>

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XI. Configure Pellet Reasoner

VIVO uses the Pellet engine to perform reasoning, which runs in the 
background at startup and also when the knowledge base is edited. VIVO 
continues serving pages while the reasoner continues working; when the
reasoner finishes, the new inferences appear. Inferred statements are cached 
in a database graph so that they are available immediately when VIVO is restarted.

By default, Pellet is fed only an incomplete view of your ontology and only 
certain inferences are materialized. These include rdf:type, 
rdfs:subClassOf,owl:equivalentClass, and owl:disjointWith. This mode is 
typically suitable for ontologies with a lot of instance data.  If you would 
like to keep the default mode, skip to the next step.

To enable "complete" OWL inference (materialize all significant entailed 
statements), open "vitro-core/webapp/config/web.xml" and search for 
PelletReasonerSetup.

Then change the name of the listener class to PelletReasonerSetupComplete. 
Because "complete" reasoning can be very resource intensive, there is also an 
option to materialize nearly all inferences except owl:sameAs and 
owl:differentFrom.

This is enabled by specifying PelletReasonerSetupPseudocomplete. For ontologies 
with large numbers of individuals, this mode can offer enormous performance 
improvements over the "complete" mode.

Finally, a class called PelletReasonerSetupPseudocompleteIgnoreDataproperties 
is provided to improve performance on ontologies with large literals where data 
property entailments are not needed.

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XII. 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

    If VIVO has an account for the user, the user will be given the privileges 
    assigned to that account.
     
    In addition, 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.
    
    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

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XIII. 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 left, 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 initialAdminUser username 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. 
* The search box is on the right side, directly opposite the "Index" link.
    Type the word "Australia" into the 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.