ARCHIVED: How can I access data in CLSD?

The Indiana University Centralized Life Sciences Data (CLSD) service was retired June 18, 2010.

For the Indiana University Centralized Life Sciences Data (CLSD) service, two categories of use are available: authenticated and unauthenticated. TeraGrid researchers may access CLSD without authentication, but such access must be conducted within the Web Services Resource Framework (WSRF) as implemented using the Perl module WSRF::Lite.

Users who have secure authentication credentials for using the Research Database Complex (RDC) at IU may access CLSD via the other supported interfaces:

• Demonstration web forms
• The AIX command-line interface
• IBM's DB2 Control Center client
• Java Database Connectivity (JDBC)
• Web Services (SOAP, etc.)

To acquire usage credentials for the RDC at IU, see Research Database Complex (RDC) usage policies. If you are a TeraGrid researcher, email Research Technologies at IU for assistance.

Using CLSD through WSRF

To use CLSD via WSRF, you must write a program that uses various WSRF protocols to interact with a Web Service running on the WSRF container running on discern.uits.iu.edu:8422. An example is presented in ARCHIVED: How do I access CLSD using WSRF? For background information about various ways of accessing CLSD data, see Making relational data available on the Grid: A survey of methods from CGI to OGSA-DAI (in .doc format).

Using CLSD via an interface requiring authentication

Once you have an account on the RDC at IU, you can access CLSD by any of the following methods:

• Use the demonstration web interface to CLSD. This demonstration service is implemented as a Java servlet; source code for the servlet is available through the CLSD page on the UITS Research Technologies web site.
  
  
• Use SSH to log into the RDC at rdc.uits.iu.edu. Start the DB2 command-line processor by running the db2 command.
  
  
• Use a desktop client, such as the IBM Control Center, that will allow you to interact with DB2.
  
  
• Write programs in Java to fetch data from the DB2 server via SQL using the Java Database Connectivity (JDBC) classes. For help, see ARCHIVED: How do I access CLSD via JDBC?
  
  
• Write programs in Perl to send queries to the DB2 server via the Perl DBI::DB2 and DBD::DB2 interfaces.
  
  
• Write Java or Perl programs that use the demonstration Web Services (JAX-RPC) interface to CLSD. (For help, see ARCHIVED: Can I access CLSD as a Web Service?) This Web Service is implemented using Apache AXIS. Source code for the service, as well as an example client that makes RPC calls to the service, is available through the CLSD page on the UITS Research Technologies web site.

To use a desktop client, you must first acquire and install special client software. DB2 clients come in two basic types: graphical and command-line oriented. Either type allows you to enter direct, ad-hoc queries; IBM provides DB2 clients for a variety of operating systems and programming languages. For example, a command-line client is available for both Unix and Windows, and a graphical client (the IBM DB2 Control Center) is available for Windows and AIX.

When you write programs to access CLSD, you can use them to build custom command-line commands, to process requests gathered from web page forms, and to execute multiple requests from CLSD.

This document was developed with support from the National Science Foundation (NSF) under Grant No. 0503697 to the University of Chicago and subcontracted to Indiana University. Additional support was provided by IU through its participation in the TeraGrid, which is supported by the NSF under Grants No. 0833618, SCI451237, SCI535258, and SCI504075. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the NSF.

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