[BioC] Using RCurl to upload CEL files to a LIMS

Seth Falcon sfalcon at fhcrc.org
Sat Mar 27 00:55:56 CET 2010

Hi Stephen,

On 3/22/10 12:37 PM, stephen at mnemosyne.co.uk wrote:
> I am trying without success to upload an Affy CEL file to a LIMS
> system using RCurl.

> The LIMS expects to receive a multipart formatted http post request
> with some metadata in the headers. When I try to create an RCurl
> statement to upload the file I get various errors complaining that
> Http GET is not supported on the server - any help or suggestions
> would be very gratefully received.

If your server wants an HTTP POST request with Content-Type: 
multipart/form-data, then maybe I can help.  Otherwise, I'm not sure I 
know what you want from your description.

Using the curl command line, I think you want something like this:

curl -F "fileOid=12345" \
      -F "analyticalGroup=bob" \
      -F "thefile=@thedata.txt" \

I think you can achieve this using RCurl as follows:

> library("RCurl")
> uri <- "http://your-server/"
> postForm(uri,
>          fileOid = "1234",
>          analyticalGroup = "bob",
>          theFile = fileUpload(filename = "~/temp/thedata.txt",
>                     contentType = "text/amazing"),
>          .encoding="uft-8")

If that does not work for you, perhaps you can try finding the right 
incantation using the curl command line.  With that, there is probably a 
way to figure out how to get RCurl to do what you want.

+ seth

Seth Falcon
Bioconductor Core Team | FHCRC

More information about the Bioconductor mailing list