[BioC] PostForm() with KEGG

[Ovokeraye Achinike-Oduaran]

Thank you so very much, Duncan. I will go get myself enlightened:).
Thanks again.

Avoks

On Mon, Feb 27, 2012 at 3:50 PM, Duncan Temple Lang
<duncan at wald.ucdavis.edu> wrote:
>
> 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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