cgi-bin/phenome/locus_pub_rank.pl

   1 #!/usr/bin/perl/
   2
   3 use strict;
   4 use warnings;
   5
   6 use CXGN::Page;
   7 use CXGN::Login;
   8 use CXGN::Apache::Error;
   9 use CXGN::DB::Connection;
  10 use CXGN::Page::FormattingHelpers qw /info_section_html
  11                                        tooltipped_text /;
  12
  13 use CXGN::Chado::Publication;
  14 use CXGN::Phenome::Locus;
  15 use CXGN::Phenome::Locus::LocusRanking;
  16
  17 my $page=CXGN::Page->new( "locus_pub_rank", "Naama");
  18
  19 my %args = $page->cgi_params(); #multi-valued parameters have values in a string, delimited by \0
  20 my $locus_id= $args{locus_id};
  21 my $dbh=CXGN::DB::Connection->new('phenome');
  22
  23 $page->jsan_use("CXGN.Phenome.Locus");
  24 $page->jsan_use("Prototype");
  25
  26
  27 my($person_id,$user_type)=CXGN::Login->new($dbh)->has_session();
  28
  29 my $locus=CXGN::Phenome::Locus->new($dbh,$locus_id);
  30 my $locus_name=$locus->get_locus_name();
  31
  32 my @assoc_pubs= $locus->get_dbxrefs_by_type('literature');
  33 $page->simple_header("Publication list for locus $locus_name", "Curator tool: Validate publications associated with locus <a href=locus_display.pl?locus_id=$locus_id target=blanc>$locus_name</a>");
  34
  35 my $locus_pub_ranks=$locus->get_locus_pub();
  36 my $pubs="";
  37 my ($val_pubs, $rej_pubs, $pending_pubs, $a_pubs)= ("" x 4);
  38
  39 my @pub;
  40
  41 foreach(sort  { $locus_pub_ranks->{$b} <=>  $locus_pub_ranks->{$a} } keys %$locus_pub_ranks )  {
  42 #foreach ( keys %$locus_pub_ranks) {
  43     my $publication=CXGN::Chado::Publication->new($dbh, $_);
  44     my $pub_id = $publication->get_pub_id();
  45     my $dbxref_id = $publication->get_dbxref_id_by_db('PMID');
  46     my $title=$publication->get_title();
  47     my $pyear=$publication->get_pyear();
  48     my $series=$publication->get_series_name();
  49     my $volume=$publication->get_volume();
  50     my $issue=$publication->get_issue();
  51     my $pages=$publication->get_pages();
  52     my $abstract= $publication->get_abstract();
  53     my $authors=$publication->get_authors_as_string();
  54     my $locusRank = CXGN::Phenome::Locus::LocusRanking->new($dbh, $locus_id, $pub_id);
  55     my $validated = $locusRank->get_validate() || "";
  56     my $score = $locusRank->get_rank();
  57
  58     my $val_form= "<BR><BR>";
  59     if ($user_type eq 'curator') {
  60         $val_form= qq|
  61         <div id='locusPubForm_$pub_id'>
  62         <div id='pub_dbxref_id_$dbxref_id'>
  63         <input type="hidden"
  64         value=$dbxref_id
  65         id="dbxref_id_$pub_id">
  66         <select id="$dbxref_id"  >
  67         <option value="" selected></option>
  68         <option value="no">no</option>
  69         <option value="yes">yes</option>
  70         <option value="maybe">maybe</option>
  71         </select>
  72         <input type="button"
  73         id="associate_pub_button"
  74         value="associate publication"
  75         onclick="Locus.addLocusDbxref('$locus_id', '$dbxref_id');this.disabled=false;">
  76         </div>
  77         </div>
  78         <BR>
  79         |;
  80     }
  81     my $associated= $publication->is_associated_publication('locus', $locus_id);
  82     my $pub_link= tooltipped_text("$authors ($pyear)",$abstract) . qq| <a href="/publication/$pub_id/view">$title.</a> $series. $volume($issue):$pages <b> Match score = $score </b> | . $val_form;
  83     if ($validated eq 'no') {
  84         $rej_pubs .= $pub_link;
  85     }elsif ($validated eq 'yes') {
  86         $val_pubs .= $pub_link;
  87     }elsif ($validated eq 'maybe') {
  88         $pending_pubs .= $pub_link;
  89     }elsif (!$associated) {
  90         $pubs .= $pub_link;
  91     }elsif ($associated) {
  92         $a_pubs .=$pub_link;
  93         print STDERR "$associated ! pub $pub_id associated with locus $locus_id\n"; }
  94 }
  95
  96
  97 print info_section_html(title   => 'Suggested publication list',
  98                         contents => $pubs,
  99                         );
 100
 101 print info_section_html(title   => 'Associated publications',
 102                         subtitle =>'(these publications are already linked with the locus, but were not validated by a curator)',
 103                         contents => $a_pubs,
 104                         );
 105
 106 print info_section_html(title   => 'Validated publications',
 107                         contents => $val_pubs,
 108                             );
 109 print info_section_html(title   => 'Pending publications',
 110                         contents => $pending_pubs,
 111                             );
 112 print info_section_html(title   => 'Rejected publications',
 113                         contents => $rej_pubs,
 114                             );
 115
 116
 117 $page->simple_footer();
 118
 119 print <<EOF;
 120 <a href="javascript:window.close();">Close This Window</a>
 121 EOF
 122