Dear Bioconductor mailing list, 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. uri <- "http://127.0.0.1:8080/tomcat/ezUploader" f = CFILE("example.CEL") fileOid="12345" analyticalGroup="12345" curlPerform(url=uri, httpheader=c(fileOid=fileOid, analyticalGroup=analyticalGroup), upload=TRUE, readdata=f@ref, infilesize=file.info(filename)[1, "size"]) An attempt to upload the given CEL file leads to a tomcat error - Apache Tomcat/6.0.18 - Error report - HTTP Status 405 - HTTP method PUT is not supported by this URL. The Java code below using the Apache HttpClient demonstrates what I am trying to achieve HttpPost httpPost = new HttpPost(url.toString()); MultipartEntity entity = new MultipartEntity(); entity.addPart("fileOid", new StringBody("12345", Charset.forName("UTF-8"))); FileBody fileBody = new FileBody(filename); entity.addPart(filename.getName(), fileBody); httpPost.setEntity(entity); Any help with the RCurl equivalent would be very gratefully received Thanks Stephen sessionInfo() R version 2.10.1 (2009-12-14) i386-apple-darwin8.11.1 locale: [1] C/UTF-8/C/C/C/C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] mnemosynePicnic_0.1.1 XML_2.6-0 RCurl_1.3-1 [4] bitops_1.0-4.1 [[alternative HTML version deleted]]

On Mon, 22 Mar 2010, stephen at mnemosyne.co.uk wrote: <snip> > HttpPost httpPost = new HttpPost(url.toString()); <snip> > Any help with the RCurl equivalent would be very gratefully received Have you played around with postForm?

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" \ http://your-server/ 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