Hi Duncan,
I finally got this to work, i.e. to extract my file two pages down. Thanks a
lot for your help. I think there is some problem with the HTML source code
of "http://www.expasy.ch/tools/protscale.html";. When I use the
getHtmlFormDescription function the output that I get is not what I would
have expected from just looking at the webpage. For e.g. there is no place
to input the sequence, only way to input is through prot_id. Also the
weight_var can essentially be linear or exponential but in this case I am
stuck with only the exponential option.
Thanks once again for your help
Regards
Sunando
On Sat, Feb 13, 2010 at 8:34 AM, Duncan Temple Lang <dun...@wald.ucdavis.edu
> wrote:
>
>
> Sunando Roy wrote:
> >
> > Hi Duncan,
> >
> > Thanks for your help. I changed the P but the output that I get is not
> > what I expect. The form gets aborted without any actual output. I get
> > the same result with
> >
> > postForm("http://www.expasy.ch/tools/protscale.html";)
>
>
> That URL (...protscale.html) is the HTML page that contains the form.
> It is not the URL to which you are supposed to submit the form request.
> That information is in the attributes of the <form ..> </form>.
> That is
>
> http://www.expasy.ch/cgi-bin/protscale.pl?1
>
> So you have to know a little about HTML forms in order to
> figure out how to map the HTML description to a request.
> That is what your browser does ( including hidden fields in
> the form, etc.)
> It is also the purpose of the R package RHTMLForms (
> www.omegahat.org/RHTMLForms
> and
> install.packages("RHTMLForms", repos = "http://www.omegahat.org/R";, type
> = "source")
> )
>
> e.g.
>
> library(RHTMLForms)
> f = getHTMLFormDescription("http://www.expasy.ch/tools/protscale.html";)
> fun = createFunction(f[[2]])
>
>
> o = fun(prot_id = "P05130", weight_var = "exponential", style = "POST")
>
> (The protscale.html is malformed with an < that messes up parsing the
> linear option.)
>
> Now, of course, you have to parse the resulting HTML (in the string given
> in the variable o)
> to get the information the form submission generated.
>
>
> D.
>
>
> >
> > just with an added message that there was no input passed on. But with
> > the input like I presented I get the same output. I could make some of
> > the examples work like for e.g
> >
> > postForm("http://www.omegahat.org/RCurl/testPassword/form_validation.cgi
> ",
> > your_name = "Duncan",
> > your_age = "35-55",
> > your_sex = "m",
> > submit = "submit",
> > .opts = list(userpwd = "bob:welcome"))
> >
> > which would suggest atleast the setup is correct.
> > I parsed the expasy protscale source code to identify the variables but
> > the form does not seem to go through. I can post the html body code if
> > needed.
> >
> > Regards
> >
> > Sunando
> > On Fri, Feb 12, 2010 at 3:54 PM, Duncan Temple Lang
> > <dun...@wald.ucdavis.edu <mailto:dun...@wald.ucdavis.edu>> wrote:
> >
> >
> >
> > Sunando Roy wrote:
> > > Hi,
> > >
> > > I am trying to submit a form to the EXPASY protscale server (
> > > http://www.expasy.ch/tools/protscale.html). I am using the RCurl
> > package and
> > > the postForm function available in it. I have extracted the
> > variables for
> > > the form from the HTML source page. According to the syntax of
> > postForm, I
> > > just need to mention the url and assign values to the input
> > mentioned in the
> > > HTML code.
> > > The code that I am using is:
> > > postForm("http://www.expasy.ch/tools/protscale.html";,
> > > "sequence" = "
> > > AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
> > > scale = "Molecular weight",
> > > window = "5",
> > > weight_edges = "100",
> > > weight_var = "linear",
> > > norm = "no",
> > > submit = "Submit"), .checkparams = TRUE)
> >
> >
> > I don't think that is what you actually submitted to R.
> > It is a syntax error as you end the cal to postForm) after "Submit"
> > and then have an extra ", .checkparams = TRUE)" afterwards.
> >
> > But, when you remove the ')' after "Submit",
> > the problem you get is that .checkparams is not a parameter
> > of postForm(), but .checkParams is. R is case-sensitive
> > so the problem is that .checkparams is being treated as a parameter
> > of your form.
> >
> > So change the p to P in .checkparams, and it works.
> >
> > D.
> >
> > > the constant error that I get is:
> > > Error in postForm("http://www.expasy.ch/tools/protscale.html";,
> > .params =
> > > list(sequence = "not", : STRING_ELT() can only be applied to a
> > 'character
> > > vector', not a 'logical'
> > >
> > > Is there any other way to submit an HTML form in R ?
> > >
> > > Thanks for the help
> > >
> > > Regards
> > >
> > > Sunando
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > R-help@r-project.org <mailto: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.
> >
> >
>
[[alternative HTML version deleted]]
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