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 Shindig-ORNG web application, and how to configure it to work with VIVO.

Table of Contents

  1. Installing and Configuring
    1. Create database tables and procedures
    2. Create configuration directory and key file
    3. Modify Tomcat settings
    4. Configure VIVO
    5. Run the deployment script
    6. Does it work?
  2. Setting up the Gadgets
    1. The orng_apps database table
    2. The orng_app_views database table

I. Installing and Configuring

I.i. Create database tables and procedures

Shindig-ORNG 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-ORNG 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-ORNG 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.

I.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-ORNG 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.

I.iii. Modify Tomcat settings

The Shindig-ORNG 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-ORNG 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-ORNG configuration file in Step I. In fact, it's more common for the setenv file to contain other parameters besides those used for Shindig-ORNG. 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'

I.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-ORNG.

Property Name Example Value
The base URL that VIVO will use when contacting the Shindig-ORNG 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 Shindig-ORNG 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

I.v. Run the deployment script

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

                ant orng

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

I.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.orng_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.

II. Setting up the Gadgets

VIVO will look at tables in MySQL to determine what gadgets should be made available, where they should appear, how big they will be, and much more. At this time, VIVO doesn't provide a user interface to edit the contents of these tables. Administrators will need to use a MySQL admin client, or SQL commands, to set these parameters.

The tables are named orng_apps and orng_app_views, and are described in the following sections.

II.i The orng_apps database table

This table acts as a dictionary of the available gadgets. Includes the name and ID of the gadget and where the source code is stored on the web. Also a flag for disabling the gadget, and some additional fields.

Field Type Usage
appid int(11) Identifies the gadget. In particular, this will be used to determine which rows in the orng_app_views table should apply to this gadget.
name varchar(255) A user-friendly name for the gadget. This will be displayed in the gadget's "Title Bar".
url varchar(255) The location where the gadget's contents and behavior are defined.
PersonFilterID int(11) unknown
enabled tinyint(1) If set to 0, this gadget will never be displayed. If set to 1, it is displayed according to the rules in the orng_app_views table.
channels varchar(255) Keywords that identify the communication channels between the gadget and VIVO.

II.ii The orng_app_views database table

Field Type Usage
appid int(11) Determines which gadget in orng_apps is affected by this rule.
viewer_req char(1) unknown
owner_req char(1) unknown
page varchar(50) What page does this rule apply to? A single gadget might have several views, but no more than one view per page. Recognized values are
  • individual -- The profile page of an individual, when it is not in "edit" mode. This applies when the viewer is not logged in, or does not have the right to edit the profile page.
  • individual-EDIT-MODE -- The profile page of an individual, when it is in "edit" mode. This applies when the viewer is logged in as an administrator or other privileged user, or as the owner of the profile page.
  • search -- The search results page.
  • gadgetDetails -- A page that contains only the selected gadget. This usually occurs when the user clicks on an icon or a link that expands the gadget to full-page mode.
view varchar(50) What is the view-mode of the gadget? These are defined as part of the OpenSocial standards.
  • profile -- The "standard" view, commonly used on the profile page of an individual
  • small -- The "condensed" view.
  • home -- The view which allows the user to change the gadget's settings.
  • canvas -- The "expanded", commonly used when the gadget is the only thing on a page.
closed_width int(11) How wide is the gadget when it is closed? (in pixels)
open_width int(11) How wide is the gadget when it is open? (in pixels)
start_closed tinyint(1) When the page is first loaded, is the gadget open or closed (1 = closed, 0 = open)
chromeId varchar(50) The gadget will be displayed on the page inside a <div> with this id. Note: the page must contain this <div> and its contents will be replaced with this gadget (or gadgets).
display_order int(11) If more than one gadget has the same chromeId, they will be displayed in order by this field.