REST access of xml.nig.ac.jp (WABI)

Created: 2008-10-14 16:17:58      Last updated: 2008-10-14 16:39:03

This workflow has a beanshell script for composing the REST URL for the services at xml.nig.ac.jp  (WABI) This URL is passed to the local worker Get_web_page_from_URL that fetches the requested data.

Note: This is a proof of concept of accessing REST services through Taverna. All of WABI's services can more easily be browsed and used in Taverna by adding their WSDL, for instance http://xml.nig.ac.jp/wsdl/GetEntry.wsdl

The example invokes the getDDBJEntry(accession) method of the getEntry service at WABI.

The workflow can be modified to invoke any other service from xml.nig.ac.jp/index.html#services by modifying the service and method parameters to the beanshell script compose_URL.

Any other input parameters to compose_URL are added to the URL as well, so if instead you want to invoke the method analyzeParamAsync(query, param) from the ClustalW service, first modify the service and method default parameters to ClustalW and analyzeParamAsync, and then edit the beanshell script's input ports:

Remove the accession port from compose_URL, then add two new input ports called query and param. (You don't need to modify the actual beanshell script as it picks up any declared input parameters.)

This pattern could probably be used for many REST services that work like xml.nig.ac.jp - but the disadvantage is that one has to manually read the documentations to figure out what the parameters are to be.

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Review Title: A breif overview

Rating: 4 out of 5

Created: 2008-10-18 14:06:30 | Updated: 2008-10-18 14:06:30

A small, yet functionally diverse, workflow that allows for REST calls to the DDBJ series of web services. Takes a little time to get your head around the functionaility of what it does and how to change the workflow inputs, but, can be used fr a range of processes.  

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  • Saturday 18 October 2008 14:04:16 (UTC)

    A very nice workflow Stian. Thank you for illustraing how Taverna can use REST.

  • Tuesday 10 March 2009 16:17:51 (UTC)

    Ace! Nice work! And I enjoyed so much my first encounterance with WHIP:)




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