paperbag has asked for the wisdom of the Perl Monks concerning the following question:

This code is returning me the web form page. I want it to submit the web form and get the actual results page, not the form page. I'm not sure what I'm doing wrong. 
use strict;
use LWP::Simple;
use URI::URL;

my $url = url("http://genome.ucsc.edu/cgi-bin/hgGateway?clade=vertebra
+te&org=0&db=0&hgsid=63734053");
$url->query_form(clade => "vertebrate",
         org => "Human",
         db => "hg17",
         position => "NM_000747",
         pix => 620,
         hgsid => 63734054,
         Submit => "submit",
         customTrackPage => "add your own custom tracks",
         hgTracksConfigPage => "configure tracks and display"     
         );

my $page = get($url);
open (OUTPUT, ">output.html") || die "Could not open output: $!\n\n";
print OUTPUT $page;

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Replies are listed 'Best First'.
Re: web form submission help
by planetscape (Chancellor) on Nov 24, 2005 at 20:25 UTC

    If possible, I would suggest using WWW::Mechanize, which offers extensive examples and many articles for reference. Nodes using WWW::Mechanize abound here on PM; Super Search will undoubtedly turn up much helpful information.

    Also, helpful modules such as HTTP::Recorder and WWW::Mechanize::Shell exist to help you automate the creation of your WWW::Mechanize scripts.


    Update: For example, using HTTP::Recorder as described here produces the following snippet:

    $agent->get('http://genome.ucsc.edu/cgi-bin/hgGateway');
$agent->form_name('mainForm');
$agent->field('clade', 'vertebrate');
$agent->field('org', 'Human');
$agent->field('db', 'hg17');
$agent->field('pix', '620');
$agent->field('position', 'NM_000747');
$agent->click('Submit');

    [download]

    And the "results" page looks something like this:

    <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<SCRIPT LANGUAGE="JavaScript">
<!-- // start
// find the top-level opener window
var opwindow = window.opener;
while (opwindow && opwindow.opener) {
  opwindow = opwindow.opener;
}
// update it with HTTP::Recorder's control panel
if (opwindow) {
 opwindow.location = "http://http-recorder";
}

// end -->
</SCRIPT>
<html>
<head>

<title>
Human NM_000747 - UCSC Genome Browser v121</title>

    <meta http-equiv="Content-Script-Type" content="text/javascript">

<link rel="STYLESHEET" href="/style/HGStyle.css?rec-url=%252Fstyle%252
+FHGStyle.css&rec-action=norecord">
<base href="http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&o
+rg=Human&db=hg17&position=NM_000747&pix=620&hgsid=63735965&Submit=sub
+mit">
</head>


<body background="../images/floret.jpg">

<h2>
Known Genes</h2>
<pre>
<tt>
<a href="hgTracks?position=chr17%3A7289129-7301656&hgsid=63735965&know
+nGene=pack&hgFind.matches=NM_000747%2C&rec-url=hgTracks%253Fposition%
+253Dchr17%253A7289129-7301656%2526hgsid%253D63735965%2526knownGene%25
+3Dpack%2526hgFind.matches%253DNM_000747%252C&rec-action=follow&rec-te
+xt=NM_000747%2520at%2520chr17%253A7289129-7301656&rec-index=1">
NM_000747 at chr17:7289129-7301656</a>
 - (NM_000747) nicotinic acetylcholine receptor beta subunit
</pre>
</tt>

<h2>
RefSeq Genes</h2>
<pre>
<tt>
<a href="hgTracks?position=chr17%3A7289129-7301656&hgsid=63735965&refG
+ene=pack&hgFind.matches=NM_000747%2C&rec-url=hgTracks%253Fposition%25
+3Dchr17%253A7289129-7301656%2526hgsid%253D63735965%2526refGene%253Dpa
+ck%2526hgFind.matches%253DNM_000747%252C&rec-action=follow&rec-text=C
+HRNB1%2520at%2520chr17%253A7289129-7301656&rec-index=1">
CHRNB1 at chr17:7289129-7301656</a>
 - (NM_000747) nicotinic acetylcholine receptor beta subunit
</pre>
</tt>


</body>

</html>

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    HTH,

    planetscape
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