[BioC] PostForm() with KEGG

[Duncan Temple Lang]

Use

   target = "alias"

in the call.

If you don't know how to map form elements to parameters in the request, you
can either read  a tutorial on HTML forms, or alternatively, use
the RHTMLForms package which you have loaded according to your search path, e.g.

  # read the form  and then turn the information into an R function.
ff = getHTMLFormDescription("http://www.genome.jp/kegg/tool/map_pathway1.html")
fun = createFunction(ff[[1]])

  # Since the action in the form is javascript, we'll provide the
  # URL manually.
u = "http://www.genome.jp/kegg-bin/search_pathway_object"
out = fun(unclassified = "ko:K01803 cpd:C00111 cpd:C00118 K00134 C00236",
          target = "alias", .url = u)

The benefits of the RHTMLForms include using the same defaults
as the form on the Web page, adding hidden parameters, identifying
the names of the parameters.

   D


On 2/27/12 3:08 AM, Ovokeraye Achinike-Oduaran wrote:
> Hi Duncan,
> 
> I noticed that with the script as is, it doesn't take into
> consideration the "include alias" checkbox. I tried modifying the
> script to force include that option but it still did not work. Any
> ideas?
> 
> u = "http://www.genome.jp/kegg-bin/search_pathway_object"
> data = postForm(u,
>                .params = list(org_name = "hsadd",
>                unclassified = paste(readLines(file.choose()), collapse = "\n"),
>                file = "", checkbox = "alias", submit = "Exec"))
> 
> 
> Thanks again.
> 
> Avoks
> 
> 
> On Mon, Feb 27, 2012 at 10:24 AM, Ovokeraye Achinike-Oduaran
> <ovokeraye at gmail.com> wrote:
>> Hi Duncan,
>>
>> Thanks a bunch.
>>
>> -Avoks
>>
>> On Fri, Feb 24, 2012 at 11:09 PM, Duncan Temple Lang
>> <duncan at wald.ucdavis.edu> wrote:
>>> Hi Avoks
>>>
>>> While the form is provided by KEGG and so bio-relatd,
>>> you might have been better posting this to the more general r-help mailing list.
>>>
>>>
>>> You are posting the HTTP request to the wrong URL. That is the URL
>>> of the Web page that displays the form, not the URL that processes
>>> the input from the form.
>>> You have to look at the JavaScript that is referenced in the action
>>> attribute of the HTML form element.
>>>
>>> The second issue is that you are submitting the name of a local file.
>>> This won't work as is.  You either need to identify this is the name of a file and not the contents
>>> of the file to send, or else send the contents.  In this form, you can send the
>>> contents via the the unclassified parameter.
>>>
>>>
>>> u = "http://www.genome.jp/kegg-bin/search_pathway_object"
>>> data = postForm(u,
>>>                .params = list(org_name = "hsadd",
>>>                               unclassified = "hsa:7167 hsa:GPI cpd:C00118\nALDOA 1.2.1.12 C00236",
>>>                               file = "", submit = "Exec"))
>>>
>>>
>>> If your input is in a file, you can use
>>>
>>>  unclassified = paste(readLines(file.choose()), collapse = "\n")
>>>
>>> as the value for the unclassified parameter.
>>>
>>>
>>> There are additional parameters that the form accepts that may be relevant for your search.
>>>
>>>
>>> As for processing the results, you will want to use
>>>
>>>  doc = htmlParse(data, asText = TRUE)
>>>
>>> and then use getNodeSet()/xpathSApply() or direct tree extraction to access the nodes you want, e.g.
>>>
>>>  xpathSApply(doc, "//li/a",  xmlGetAttr, "href")
>>>
>>>
>>>  D.
>>>
>>>
>>> On 2/24/12 6:09 AM, Ovokeraye Achinike-Oduaran wrote:
>>>> Hi all,
>>>>
>>>> I am trying to use postForm() with the KEGG website but I am stuck on
>>>> how to get my results. Is it possible (code below) or am I using
>>>> postForm() wrongly? The code appears to run but I'm not quite sure how
>>>> to read the results assuming there are any. Please help.
>>>>
>>>> Thanks.
>>>>
>>>> Avoks
>>>> ____
>>>>
>>>> data = postForm("http://www.genome.jp/kegg/tool/map_pathway1.html",
>>>> org_name = "hsadd",
>>>> file = file.choose(),
>>>> submit = "Exec")
>>>>
>>>>> sessionInfo()
>>>> R version 2.14.1 (2011-12-22)
>>>> Platform: i386-pc-mingw32/i386 (32-bit)
>>>>
>>>> locale:
>>>> [1] LC_COLLATE=English_xxx.1252  LC_CTYPE=English_xxx.1252
>>>> [3] LC_MONETARY=English_xxx.1252 LC_NUMERIC=C
>>>> [5] LC_TIME=English_xxx.1252
>>>>
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>
>>>> other attached packages:
>>>> [1] RHTMLForms_0.5-1 XML_3.9-4.1      RCurl_1.91-1.1   bitops_1.0-4.1
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] tools_2.14.1
>>>>
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>>>
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