On 07/03/2010 10:59 PM, Brad McNeney wrote:
> The following call to curl fetches me the information I want (as html)
> from a webserver:
>
> curl -F list_file=@snptxt -F html_output=on
> http://integrin.ucd.ie/cgi-bin/rs2cm.cgi
>
> The file snptxt is a plain-text file in my working directory with the
> following two lines:
>
> rs6598
> rs123456
>
>
> In R I try to replicate this with RCurl as follows:
>
> require(RCurl)
> postForm(uri="http://integrin.ucd.ie/cgi-bin/rs2cm.cgi",
> "list_file"="@snptxt", "html_output"="on")
>
> but the table that is supposed to contain my results is empty (table
> caption is Genetic Locations). The cgi script has apparently received
> the html_output=on information though.
>
Hi Brad
I think the path to the file to be uploaded needs to be wrapped in a
call to fileUpload, along the lines of
postForm(uri="http://integrin.ucd.ie/cgi-bin/rs2cm.cgi",
list_file=fileUpload("/tmp/snp.txt"), html_output="on")
Martin
> I get the same results on Linux and Windows -- sessionInfo() for both
> follows. Any pointers appreciated.
>
> Thanks,
>
> Brad
> ---
> Brad McNeney
> Statistics and Actuarial Science
> Simon Fraser University
>
> Linux:
>
>> sessionInfo()
> R version 2.11.0 (2010-04-22)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] XML_3.1-0 RCurl_1.4-2 bitops_1.0-4.1
>
> Windows:
>
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252
> [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
> [5] LC_TIME=English_Canada.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] XML_3.1-0 RCurl_1.4-2 bitops_1.0-4.1
>
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> and provide commented, minimal, self-contained, reproducible code.
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793