cgi-bin/phenome/locus_pub_rank.pl

   1 #!/usr/bin/perl/
   2
   3
   4 use strict;
   5
   6 use CXGN::Page;
   7 #use CXGN::Page::Simple;
   8 #use CXGN::Page::VHost::SGN;
   9 use CXGN::Login;
  10 use CXGN::Apache::Error;
  11 use CXGN::DB::Connection;
  12 use CXGN::Page::FormattingHelpers qw /info_section_html
  13                                        tooltipped_text /;
  14
  15 use CXGN::Chado::Publication;
  16 use CXGN::Phenome::Locus;
  17 use CXGN::Phenome::Locus::LocusRanking;
  18
  19 my $page=CXGN::Page->new( "locus_pub_rank", "Naama");
  20
  21 my %args = $page->cgi_params(); #multi-valued parameters have values in a string, delimited by \0
  22 my $locus_id= $args{locus_id};
  23 my $dbh=CXGN::DB::Connection->new('phenome');
  24
  25 $page->jsan_use("CXGN.Phenome.Locus");
  26 $page->jsan_use("Prototype");
  27
  28
  29 my($person_id,$user_type)=CXGN::Login->new($dbh)->has_session();
  30
  31 my $locus=CXGN::Phenome::Locus->new($dbh,$locus_id);
  32 my $locus_name=$locus->get_locus_name();
  33
  34 my @assoc_pubs= $locus->get_dbxrefs_by_type('literature');
  35 $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>");
  36
  37 my $locus_pub_ranks=$locus->get_locus_pub();
  38 my $pubs="";
  39 my ($val_pubs, $rej_pubs, $pending_pubs, $a_pubs)= ("" x 4);
  40
  41 my @pub;
  42
  43 foreach(sort  { $locus_pub_ranks->{$b} <=>  $locus_pub_ranks->{$a} } keys %$locus_pub_ranks )  {
  44 #foreach ( keys %$locus_pub_ranks) {
  45     my $publication=CXGN::Chado::Publication->new($dbh, $_);
  46     my $pub_id = $publication->get_pub_id();
  47     my $dbxref_id = $publication->get_dbxref_id_by_db('PMID');
  48     my $title=$publication->get_title();
  49     my $pyear=$publication->get_pyear();
  50     my $series=$publication->get_series_name();
  51     my $volume=$publication->get_volume();
  52     my $issue=$publication->get_issue();
  53     my $pages=$publication->get_pages();
  54     my $abstract= $publication->get_abstract();
  55     my $authors=$publication->get_authors_as_string();
  56     my $locusRank = CXGN::Phenome::Locus::LocusRanking->new($dbh, $locus_id, $pub_id);
  57     my $validated = $locusRank->get_validate() || "";
  58     my $score = $locusRank->get_rank();
  59
  60     my $val_form= "<BR><BR>";
  61     if ($user_type eq 'curator') {
  62         $val_form= qq|
  63         <div id='locusPubForm_$pub_id'>
  64         <div id='pub_dbxref_id_$dbxref_id'>
  65         <input type="hidden"
  66         value=$dbxref_id
  67         id="dbxref_id_$pub_id">
  68         <select id="$dbxref_id"  >
  69         <option value="" selected></option>
  70         <option value="no">no</option>
  71         <option value="yes">yes</option>
  72         <option value="maybe">maybe</option>
  73         </select>
  74         <input type="button"
  75         id="associate_pub_button"
  76         value="associate publication"
  77         onclick="Locus.addLocusDbxref('$locus_id', '$dbxref_id');this.disabled=false;">
  78         </div>
  79         </div>
  80         <BR>
  81         |;
  82     }
  83     my $associated= $publication->is_associated_publication('locus', $locus_id);
  84     my $pub_link= tooltipped_text("$authors ($pyear)",$abstract) . qq| <a href="/chado/publication.pl?pub_id=$pub_id">$title.</a> $series. $volume($issue):$pages <b> Match score = $score </b> | . $val_form;
  85     if ($validated eq 'no') {
  86         $rej_pubs .= $pub_link; #qq|<a href="/chado/publication.pl?pub_id=$pub_id">$title</a> ($pyear) $val_form |;
  87     }elsif ($validated eq 'yes') {
  88         $val_pubs .= $pub_link;
  89     }elsif ($validated eq 'maybe') {
  90         $pending_pubs .= $pub_link;
  91     }elsif (!$associated) {
  92         $pubs .= $pub_link;
  93     }elsif ($associated) {
  94         $a_pubs .=$pub_link;
  95         print STDERR "$associated ! pub $pub_id associated with locus $locus_id\n"; }
  96 }
  97
  98
  99 print info_section_html(title   => 'Suggested publication list',
 100                         contents => $pubs,
 101                         );
 102
 103 print info_section_html(title   => 'Associated publications',
 104                         subtitle =>'(these publications are already linked with the locus, but were not validated by a curator)',
 105                         contents => $a_pubs,
 106                         );
 107
 108 print info_section_html(title   => 'Validated publications',
 109                         contents => $val_pubs,
 110                             );
 111 print info_section_html(title   => 'Pending publications',
 112                         contents => $pending_pubs,
 113                             );
 114 print info_section_html(title   => 'Rejected publications',
 115                         contents => $rej_pubs,
 116                             );
 117
 118
 119 $page->simple_footer();
 120
 121 print <<EOF;
 122 <a href="javascript:window.close();">Close This Window</a>
 123 EOF
 124