Setting up VIVO to use OpenSocial Gadgets

Instructions for connecting VIVO and Open Research Networking Gadgets

This document contains instructions on how to configure your VIVO installation to use OpenSocial gadgets.

VIVO uses an extension of the OpenSocial protocols called Open Research Networking Gadgets, or ORNG. ORNG is a project of the Clinical & Translational Science Institute at the University of California, San Francisco. You can find out more about the ORNG project at their web site, http://www.opengadgets.org/index.html

ORNG supports gadgets using a modified version of Apache Shindig. These instructions tell you how to install the ORNG Shindig web application, and how to configure it to work with VIVO.

Create database tables and procedures
Create configuration directory and key file
Modify Tomcat settings
Configure VIVO
Run the deployment script
Does it work?

I. Create database tables and procedures

Shindig uses several database tables in MySQL to store its data: which gadgets appear on which pages, how large are the gadgets, what information applies to each individual, and more. Shindig also creates stored procedures in MySQL. These are small pieces of code that simplify the use of the database tables.

In the VIVO distribution directory, a file called vitro-core/opensocial/shindig_orng_tables.sql contains SQL commands that create the tables and stored procedures for Shindig to use.

Tell MySQL to process this file with a command like this:

mysql -u username -p database < sql_file

So, if your current directory is the VIVO distibution directory, and your VIVO database is vivoDb and your MySQL user account is vivoUser, then you might use the command this way:

mysql -u vivoUser -p vivoDb < vitro-core/opensocial/shindig_orng_tables.sql

MySQL will prompt you for the password for your MySQL user account, and then process the file.

You may want to start your gadget collection with some example gadgets that have been developed by the ORNG group. The file called vitro-core/opensocial/shindig_example_gadgets.sql contains SQL commands that will add these gadgets to your system's configuration.

If you want to load these example gadgets, you can use a command similar to the previous one:

mysql -u vivoUser -p vivoDb < vitro-core/opensocial/shindig_example_gadgets.sql

As before, MySQL will prompt you for the password for your MySQL user account, and then process the file.

II. Create configuration directory and key file

In your VIVO home directory, create a directory called shindig. Under that, create directories called conf and openssl. Your VIVO home directory will look something like this:

     [VIVO home directory]
      |
      |--shindig
      |   |
      |   |--conf
      |   |
      |   |--openssl
      |
      |--solr
      |
      |--uploads

Shindig uses an encryption key to insure that the communication between the gadget and the server is secure. You should create a file that contains the encryption key, and store that file in the shindig/openssl directory that you created.

On Unix-based systems (like Linux or Mac OS X), this command will create an encryption key from a random seed:

dd if=/dev/random bs=32 count=1 | openssl base64 > [key-file]

For example, if your VIVO home directory is /usr/local/vivo/data, you might use the command this way:

dd if=/dev/random bs=32 count=1 | openssl base64 > /usr/local/vivo/data/shindig/openssl/securitytokenkey.txt

If your VIVO installation is installed on a machine that runs Microsoft Windows, you will need to find another way to create an encryption key. The easiest way might be to find a Unix-based machine, issue the command above, and copy the resulting file to your Windows machine.

III. Modify Tomcat settings

The Shindig application must know where to find the configuration file that you created in Step I. It must also know its own URL, so that URL can be inserted into the gadgets.

This information is provided through startup parameters in Tomcat. With most installations of Tomcat, the "setenv.sh" or "setenv.bat" file in Tomcat's bin directory is a convenient place to set these parameters. If this file does not exist in Tomcat's bin directory, you can create it.

Here is an example of the setenv file, showing only the Shindig requirements:

export CLASSPATH=/usr/local/vivo/data/shindig/conf
export CATALINA_OPTS='-Dshindig.host=localhost -Dshindig.port=8080'

This assumes that your setenv file was empty before starting this process, and that you used the default location for the Shindig configuration file in Step I. In fact, it's more common for the setenv file to contain other parameters besides those used for Shindig. In that case, it might look more like this:

export CLASSPATH=/usr/local/vivo/data/shindig/conf
export CATALINA_OPTS='-Dshindig.host=localhost -Dshindig.port=8080 -Djava.awt.headless=true -Xms1024m -Xmx1024m -XX:MaxPermSize=128m'

IV. Configure VIVO

In the VIVO distribution directory, the file called deploy.properties contains configuration options for the VIVO application. You must set some additional parameters so VIVO will be able to communicate with Shindig.

Property Name	Example Value
The base URL that VIVO will use when contacting the ORNG Shindig application. Usually, this is the same host and port number as VIVO itself, with a context path of shindigorng
OpenSocial.shindigURL	http://localhost:8080/shindigorng
The host name and port number of the Token Service that ORNG shindig creates. Note that a value of localhost or 127.0.0.1 will not work. You must provide the actual host name of your machine, followed by :8777
OpenSocial.tokenService	myhost.mydomain.edu:8777
The path to a key file that will be used to generate security tokens. This is the file that was created in Step I of this process.
OpenSocial.tokenKeyFile	/usr/local/vivo/data/shindig/openssl/securitytokenkey.txt

V. Run the deployment script

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

                ant orng

to configure the ORNG Shindig application and deploy it to Tomcat's webapps directory.

VI. Does it work?

Start VIVO. Enter a search term in the search box, and view the results. Check the gadgets there. Navigate to a person's profile page. Again, check for the expected gadgets.

If the gadgets do not appear as you expect, look for these symptoms, and check for the corresponding possible causes.

Symptoms	Possible causes
Gadgets do not appear on Individual page or in search results. Tomcat "localhost" log file contains an error message: Unable to load properties: shindig.orng.properties	Configuration file is not correctly named. Tomcat's setenv file does not specify the correct CLASSPATH

Dialog box appears in the browser with the message: "Error 500 reading application data: internalError" Tomcat "catalina" log file contains an error message: java.sql.SQLException: Access denied for user	Configuration file contains incorrect value for one or more of these: orng.dbURL orng.dbUser orng.dbPassword

"Smoke tests" fail at startup. Token key file for Shindig does not exist Pages that display gadgets "hang" in the browser. Tomcat "localhost" log file contains error messages, including: com.google.inject.CreationException: Guice creation errors	OpenSocial.tokenKeyFile is not set in deploy.properties, or the file does not exist at the specified location.

Gadgets do not appear on Individual page or in search results vivo.all.log contains an error message: MySQLSyntaxErrorException: Table 'vivo.shindig_apps' doesn't exist	MySQL does not contain the shindig tables. shindig_orng_tables.sql was not processed.

Gadgets do not appear on Individual page or in search results vivo.all.log contains an error message: java.net.ConnectException: Connection refused	In deploy.properties, OpenSocial.tokenService is not set correctly.