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Revision 1.5 - (download) (annotate)
Wed Oct 12 21:03:16 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-00-00-00
Changes since 1.4: +1 -1 lines
Broad minor fixes to make the SEED use relative paths throughout.

(The motivation this is to fully enable hiding the actual location of a running SEED system behind a web proxy so that things like NMPDR protein page references can be made stable across multiple releases).

This involved things like the following:

Changing $cgi->url() to $cgi->url(-relative => 1)
Changing $cgi->self_url() to $cgi->url(-relative => 1, -query => 1, -path_info => 1)

Changing the definition of FIG::cgi_url() to return "." (this may break something, but I haven't found it yet).

use FIG;
my $fig = new FIG;
use HTML;
use CGI;

my $cgi = new CGI;
my $html = [];

if($cgi->param('genome') && $cgi->param('attribute') && $cgi->param('value'))
        push (@$html, "<TITLE>Connect Pegs with Attributes to Subsystems</TITLE>");
        my $genome_string = $cgi->param('genome');
	my @string_parts = split(", ",$genome_string);
        my $genome = $string_parts[1]; 
	my $att_param = $cgi->param('attribute');
	my $value_param = $cgi->param('value');
	my @pegs = $fig->pegs_of($genome);
        my %list_of_ss; 
 	foreach my $peg (@pegs) {
  		next unless (my @attr=$fig->get_attributes($peg));
  		foreach my $attr (@attr) {
   			next unless (defined $attr);
        		my ($gotpeg, $tag, $val, $link)=@$attr;
	                $tag = uc($tag);
			next unless ($tag eq $att_param);
			next unless($val eq $value_param);
			my @subsystems = $fig->subsystems_for_peg($peg);
			foreach my $ss (@subsystems)
		 		my $ss_name = $ss->[0];
                 		$list_of_ss{$ss_name} = "1";
        my @list = keys(%list_of_ss);
	my $prefix = &FIG::cgi_url(-relative => 1) . "/subsys.cgi?user=&ssa_name=";
	my $suffix = "&request=show_ssa";	
        foreach my $s (@list)
	   my $url = "<a href='$prefix.$s.$suffix'>$s</a>";	    

	$html = [];
	push @$html, "<TITLE>Connect Pegs with Attributes to Subsystems</TITLE>";

	push(@$html,$cgi->start_form(-action => "ma2sub.cgi",  -method => 'post'));

	my @gs_list;
	my @genomes = $fig->genomes('complete');
	foreach $g (@genomes){
		my $gs = $fig->genus_species($g);
		push(@gs_list, $gs.", ".$g);

	@gs_list2 =sort {uc($a) cmp uc($b)} @gs_list;
     		$cgi->h3("select genome"),
     		$cgi->scrolling_list(-name => 'genome',
			  -values => [@gs_list2],
			  -size => 10,
			   -multiple => 1

	#my $opt=$fig->get_keys("peg"); # all the peg tags
	#my @options=sort {uc($a) cmp uc($b)} keys %$opt;
	#unshift(@options, undef); 
	@options =("microarray_sigmaB_regulon","pH_75_vs_55");
	push(@$html,$cgi->h3("select experiment"), $cgi->popup_menu(-name => 'attribute', -values=>\@options), $cgi->br, $cgi->hr);

	@options2 = ("up regulated","down regulated");
	push(@$html,$cgi->h3("select value"), $cgi->popup_menu(-name => 'value', -values=>\@options2), $cgi->br,$cgi->hr);

	push(@$html,$cgi->submit('find subsystems'), $cgi->end_form);



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