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Revision 1.4 - (download) (annotate)
Fri Sep 15 02:25:16 2006 UTC (13 years, 2 months ago) by hwang
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.3: +3 -3 lines
fix grammatical error

#/usr/bin/perl
use FIG;
use strict;
use CGI;
use FigWebServices::SeedComponents::PubMed;

my $cgi =  new CGI;
my $fig =  new FIG;

print $cgi->header;
print $cgi->start_html( -title=>'Literature for peg',
			-style=>{ -src => 'Html/dnd.css'},
			  );

	
my $id_string = $cgi->param("ids");
my $peg = $cgi->param("peg");

if (!$id_string) {
	print "Literature found for this peg was not specific to this peg<p>";
	exit;
	}	


print "<table>";
print "<tr><td bgcolor=#D2E6F0>Peg</td><td> $peg</td></tr>";
my $role = $fig->function_of($peg);
print "<tr><td bgcolor=#D2E6F0>Functional Role</td><td> $role</td></tr></table>";

print $cgi->hr();
print "<I>Getting PubMed literature for $id_string ...</I><p>";

my $pmid_output = &FIG::run_gathering_output("$FIG_Config::bin/get_pubmed_journals", $id_string);

my @journals_list = split(/ /, $pmid_output);
my %journals_list_seen = ();

foreach (@journals_list) {
 	$journals_list_seen{$_} = $_;
	#print "journals here are $_\n";
}

#Add PubMed Attributes here
my @pubmed_attributes = $fig->get_attributes($peg, "PUBMED");
foreach (@pubmed_attributes) {

	my @line = @{$_};
	#print "id is $line[2]\n";
	if (! $journals_list_seen{$line[2]} ) {
	        #print "pushing\n";
		push (@journals_list, $line[2]);
	}
}


my @new_journals = &FigWebServices::SeedComponents::PubMed::sort_journals(\@journals_list);
my $journal_htmltable = &FigWebServices::SeedComponents::PubMed::journals_as_htmltable(\@new_journals);

#Put journals as a string to be passed the next cgi 

my $journal_info;
my %journals_seen = ();

foreach (@new_journals) {
	my($pmid, $year,$month,$date,$title) = split(/\t/,$_);
	my $j = "$pmid|$title";
	$journal_info .= $j.";";
	$journals_seen{$pmid} = $title;
}

my @attributes = $fig->get_attributes($peg);
my @relevant;
my @notrelevant;
my @notcurated;

foreach (@attributes) {
	my @att_line = @{$_};
	my $key = $att_line[1];
	my ($pmid, $title)  = split(/\,/,$att_line[2]);
	
	if ($key =~ m/\_RELEVANT\_CURATED\_BY\_(.*)/) {
	my $anno_name = $1;
	my $pmid_name = "$pmid($anno_name)";
	push (@relevant, $pmid_name);
	delete $journals_seen{$pmid};
	}	
	
	if ($key =~ m/\_NOTRELEVANT\_CURATED\_BY\_(.*)/) {
	my $anno_name = $1;
	my $pmid_name = "$pmid($anno_name)";
	push (@notrelevant, $pmid_name);
	delete $journals_seen{$pmid};
	}	

	if ($key =~ m/\_NOT\_CURATED\_/) {
		if($journals_seen{$pmid}) {
		  delete $journals_seen{$pmid};
		}	
		else {	
	  	$journals_seen{$pmid};
  		}
	}	
}
#original div
my $journal_div;
my $journal_relevant_div;
my $journal_notrelevant_div;

foreach (@notrelevant) {
    $journal_notrelevant_div .= "<li id=\"$_\">$_</li>";
}

foreach (@relevant) {
    $journal_relevant_div .= "<li id=\"$_\">$_</li>";
}

while( my($k,$v) = each(%journals_seen)) {
	$journal_div .=	"<li id=\"$k\">$k</li>";	
}

#not curated div


print $journal_htmltable;

if ($#journals_list < 0) {
	print "Literature found for this peg was not specific to this peg<p>";
	
	}	

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