Hi, I am trying to use a CGI service (Pubchem PUG) via RCurl and am
running into a problem where the data must be supplied via POST - but
I don't know the keyword for the argument.
The data to be sent is an XML fragment. I can do this via the command
line using curl: I save the XML string to a file called query.xml and
then do
curl -d @query.xml "http://pubchem.ncbi.nlm.nih.gov/pug/pug.cgi";
I get the expected response. More importantly, the verbose option shows:
> Accept: */*
> Content-Length: 1227
> Content-Type: application/x-www-form-urlencoded
However, when I try to do this via RCurl, the data doesn't seem to get
sent:
q <- "<PCT-Data> <PCT-Data_input> <PCT-InputData> <PCT-
InputData_query> <PCT-Query> <PCT-
Query_type> <PCT-QueryType> <PCT-
QueryType_qas> <PCT-
QueryActivitySummary> <PCT-
QueryActivitySummary_output value=\"summary-table\">0</PCT-
QueryActivitySummary_output> <PCT-
QueryActivitySummary_type value=\"assay-central\">0</PCT-
QueryActivitySummary_type> <PCT-
QueryActivitySummary_scids> <PCT-
QueryUids> <PCT-
QueryUids_ids> <PCT-ID-
List> <PCT-ID-List_db>pccompound</PCT-ID-
List_db> <PCT-ID-
List_uids> <PCT-ID-List_uids_E>3243128</PCT-
ID-List_uids_E> </PCT-ID-
List_uids> </PCT-ID-List>
</PCT-QueryUids_ids> </PCT-
QueryUids> </PCT-
QueryActivitySummary_scids> </PCT-
QueryActivitySummary> </PCT-QueryType_qas> </
PCT-QueryType> </PCT-Query_type> </PCT-Query> </
PCT-InputData_query> </PCT-InputData> </PCT-Data_input></PCT-Data>"
> postForm(url, q, style="post", .opts = list(verbose=TRUE))
* About to connect() to pubchem.ncbi.nlm.nih.gov port 80 (#0)
* Trying 130.14.29.110... * connected
* Connected to pubchem.ncbi.nlm.nih.gov (130.14.29.110) port 80 (#0)
> POST /pug/pug.cgi HTTP/1.1
Host: pubchem.ncbi.nlm.nih.gov
Accept: */*
Content-Length: 0
Content-Type: application/x-www-form-urlencoded
As you can see, the data in q doesn't seem to get sent (content-length
= 0).
Does anybody have any suggestions as to why the call to postForm
doesn't work, but the command line call does?
Thanks,
----------------------------------------------------
Rajarshi Guha | NIH Chemical Genomics Center
http://www.rguha.net | http://ncgc.nih.gov
----------------------------------------------------
Q: Why did the mathematician name his dog "Cauchy"?
A: Because he left a residue at every pole.
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
