cgi-bin/search/pub_search.pl

   1 use strict;
   2 use warnings;
   3
   4 use CXGN::Publication;
   5 use CXGN::Page;
   6 use CXGN::Page::FormattingHelpers qw/
   7   blue_section_html
   8   info_section_html
   9   page_title_html
  10   columnar_table_html
  11   /;
  12 use CXGN::Search::CannedForms;
  13 use CXGN::DB::Connection;
  14 use CXGN::Login;
  15 use CXGN::People::Person;
  16 use CXGN::Chado::Publication;
  17
  18 #################################################
  19
  20 # Start a new SGN page.
  21
  22 my $page = CXGN::Page->new( "SGN publcation search results", "Naama" );
  23
  24 $page->jsan_use("jquery");
  25 $page->jsan_use("CXGN.Phenome.Publication");
  26
  27 $page->header();
  28
  29 print page_title_html('SGN Publication search');
  30 my $dbh = CXGN::DB::Connection->new;
  31
  32 #create the search and query objects
  33 my $search = CXGN::Publication->new;
  34 my $query  = $search->new_query;
  35
  36 $search->page_size(10);    #set 10 phenetypes per page
  37
  38 my ( $login_person_id, $login_user_type ) =
  39   CXGN::Login->new($dbh)->has_session();
  40
  41 #get the parameters
  42 my %params = $page->get_all_encoded_arguments;
  43
  44 #my $allele_keyword = $page->get_encoded_arguments("allele_keyword");
  45 $query->from_request( \%params );
  46
  47 if (%params) {
  48     $query->order_by( date_stored => 'desc', pyear => 'desc', title => '' );
  49     my $result = $search->do_search($query);    #execute the search
  50     my @results;
  51
  52     ###check if the the user has permission to alter pub_curator status
  53
  54     my $has_permission = 0;
  55     if (   $login_user_type eq 'curator'
  56         || $login_user_type eq 'submitter'
  57         || $login_user_type eq 'sequencer' )
  58     {
  59         $has_permission = 1;
  60     }
  61     #####
  62
  63     while ( my $r = $result->next_result ) {
  64         my $pub_id      = $r->[0];
  65         my $publication = CXGN::Chado::Publication->new( $dbh, $pub_id );
  66         my $pub_ref     = $publication->print_mini_ref();
  67
  68         #my $title= $r->[1];
  69         #my $series = $r->[2];
  70         #my $pyear= $r->[3];
  71         my $assigned_to_id = $r->[4];
  72         my $assigned_to =
  73           CXGN::People::Person->new( $dbh, $assigned_to_id )->get_first_name();
  74         my $curation_date = $r->[5];
  75         my $curated_by_id = $r->[6];
  76         my $stat          = $r->[7];
  77         my $stored_on     = $r->[8];
  78         $stored_on =~ s/(\d{4}-\d{2}-\d{2})(.*)/$1/;
  79
  80         my @stat_options = ( "curated", "pending", "irrelevant", "no gene" );
  81         my $stat_options = qq|<option value=""></option>|;
  82         foreach my $s (@stat_options) {
  83             my $selected = qq|selected="selected"| if $s eq $stat || '';
  84             $stat_options .= qq|<option value="$s" $selected >$s</option>|;
  85         }
  86         my $stats = $stat;
  87         $stats =
  88 qq|<select id="pub_stat" onchange="Publication.updatePubCuratorStat(this.value, $pub_id)">
  89                     $stat_options
  90                     </select>
  91                    | if $has_permission;
  92
  93         my @curators = CXGN::People::Person::get_curators($dbh);
  94         my %names =
  95           map { $_ => CXGN::People::Person->new( $dbh, $_ )->get_first_name() }
  96           @curators;
  97         my $curator_options = qq|<option value=""></option>|;
  98         for my $curator_id ( keys %names ) {
  99             my $curator  = $names{$curator_id};
 100             my $selected = qq|selected="selected"| if $curator_id == $assigned_to_id || '';
 101             $curator_options .=
 102               qq|<option value="$curator_id" $selected>$curator</option>|;
 103         }
 104         my $curators = $assigned_to;
 105         $curators =
 106 qq|<select id="pub_curator_select" onchange="Publication.updatePubCuratorAssigned(this.value, $pub_id)">
 107                      $curator_options
 108                      </select>
 109                     | if $has_permission;
 110
 111         my $pub = CXGN::Chado::Publication->new( $dbh, $pub_id );
 112         push @results,
 113           [
 114             map { $_ } (
 115                 qq|<a href="/chado/publication.pl?pub_id=$pub_id">$pub_ref</a>|,
 116                 $stats, $curators, $stored_on
 117             )
 118           ];
 119     }
 120
 121     #build the HTML to output
 122     my $pagination_html = $search->pagination_buttons_html( $query, $result );
 123
 124     my $results_html = <<EOH;
 125     <div id="searchresults">
 126 EOH
 127
 128     $results_html .= columnar_table_html(
 129         headings   => [ 'Title', 'Status', 'Assigned to', 'Stored' ],
 130         data       => \@results,
 131         __alt_freq => 2,
 132         __align    => 'llll'
 133
 134           # __alt_width => 2,
 135     );
 136
 137     $results_html .= <<EOH;
 138 </div>
 139 $pagination_html
 140 EOH
 141
 142     if (@results) {
 143         print blue_section_html(
 144             'Publication search results',
 145             ,
 146             sprintf(
 147                 '<span class="paginate_summary">%s matches </span>',
 148                 $result->total_results, $result->time
 149             ),
 150             $results_html
 151         );
 152     }
 153     else {
 154         print '<h4>No matches found</h4>';
 155     }
 156
 157     print info_section_html(
 158         title => 'Search again',
 159         contents =>
 160           CXGN::Search::CannedForms::publication_search_form( $page, $query )
 161     );
 162
 163 }
 164 else {
 165     print CXGN::Search::CannedForms::publication_search_form($page);
 166 }
 167
 168 $page->footer();
 169
 170 #############
 171