[BioC] Using RCurl and XML to access an API

[Hervé Pagès]

Hi Aaron,

This kind of operations (retrieving XML docs from the web
and parsing their content) is at the heart of some Bioconductor
packages like biomaRt or rtracklayer:

   http://bioconductor.org/packages/release/bioc/html/biomaRt.html
   http://bioconductor.org/packages/release/bioc/html/rtracklayer.html

Maybe you could have a look at how things are done in those
packages so you get an idea of how that works.

Cheers,
H.


Aaron Wolen wrote:
> I'd like to access an API from within R but I'm not sure how to do so. The
> API uses HTTP and supports both POST and PUT methods. I'm able to access it
> successfully from the terminal using the following curl command:
> curl --data @genes.xml http://api-url
> 
> Where genes.xml is a local file containing the genes I want to submit and
> http://api-url is the API's address. However, I'm not sure how to replicate
> this command in R. The request payload and response payload are both XML
> streams, so I'm fairly certain this will require a combination of the RCurl
> and XML packages, but I've had no luck getting RCurl to work. I'd really
> appreciate some help with this.
> 
> Thanks,
> Aaron
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Hervé Pagès

Program in Computational Biology
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