problem post request with RCurl

Wed, Nov 18, 2009 8:18 PM

Use

 curlPerform(url = 'http://pubchem.ncbi.nlm.nih.gov/pug/pug.cgi', postfields = q)


That gives me:

<PCT-Data>
  <PCT-Data_output>
    <PCT-OutputData>
      <PCT-OutputData_status>
        <PCT-Status-Message>
          <PCT-Status-Message_status>
            <PCT-Status value="running"/>
          </PCT-Status-Message_status>
        </PCT-Status-Message>
      </PCT-OutputData_status>
      <PCT-OutputData_output>
        <PCT-OutputData_output_waiting>
          <PCT-Waiting>
            <PCT-Waiting_reqid>31406321645402938</PCT-Waiting_reqid>
          </PCT-Waiting>
        </PCT-OutputData_output_waiting>
      </PCT-OutputData_output>
    </PCT-OutputData>
  </PCT-Data_output>
</PCT-Data>

Rajarshi Guha wrote:

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.

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problem post request with RCurl

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