lib/CXGN/Publication.pm

   1 use strict;
   2
   3 ####################
   4
   5 package CXGN::Publication;
   6 use base qw/CXGN::Search::DBI::Simple CXGN::Search::WWWSearch/;
   7
   8 __PACKAGE__->creates_result('CXGN::Publication::Result');
   9 __PACKAGE__->uses_query('CXGN::Publication::Query');
  10
  11 #####################
  12
  13 package CXGN::Publication::Result;
  14 use base qw/CXGN::Search::BasicResult/;
  15
  16 #####################
  17
  18 package CXGN::Publication::Query;
  19 use CXGN::Page::FormattingHelpers
  20   qw(
  21      simple_selectbox_html
  22      info_table_html
  23      hierarchical_selectboxes_html
  24      conditional_like_input_html
  25      html_optional_show
  26     );
  27
  28 use base qw/CXGN::Search::DBI::Simple::WWWQuery/;
  29 our %pname;
  30
  31 sub _cached_dbh() { our $_cached_dbc ||= CXGN::DB::Connection->new('public') }
  32 my $public = 'public';
  33 my $sgn_people= 'sgn_people';
  34 my $phenome=  'phenome';
  35 __PACKAGE__->selects_data("$public.pub.pub_id","$public.pub.title","$public.pub.series_name", "$public.pub.pyear","$phenome.pub_curator.assigned_to","$phenome.pub_curator.date_curated", "$phenome.pub_curator.curated_by", "$phenome.pub_curator.status", "$phenome.pub_curator.date_stored" );
  36
  37
  38 __PACKAGE__->join_root("$public.pub");
  39
  40 __PACKAGE__->uses_joinpath('authorpath',
  41                            ["$public.pubauthor", "$public.pubauthor.pub_id = $public.pub.pub_id"],
  42     );
  43
  44 __PACKAGE__->uses_joinpath('curatorpath',
  45                            [ "$phenome.pub_curator", "$phenome.pub_curator.pub_id=$public.pub.pub_id" ],
  46                            [ "$sgn_people.sp_person", "$phenome.pub_curator.assigned_to = $sgn_people.sp_person.sp_person_id" ],
  47                            );
  48
  49
  50 __PACKAGE__->has_parameter(name   =>'author',
  51                            columns=>["$public.pubauthor.surname",
  52                                      "$public.pubauthor.givennames"],
  53                            sqlexpr=>"$public.pubauthor.surname || $public.pubauthor.givennames",
  54                            );
  55
  56 __PACKAGE__->has_parameter(name   =>'title',
  57                            columns=>"$public.pub.title",
  58     );
  59 __PACKAGE__->has_parameter(name   =>'pyear',
  60                            columns=>"$public.pub.pyear",
  61     );
  62 __PACKAGE__->has_parameter(name   =>'series',
  63                            columns=>"$public.pub.series_name",
  64     );
  65
  66 __PACKAGE__->has_parameter(name   =>'assigned_to',
  67                            columns=>["$sgn_people.sp_person.first_name",
  68                                      "$sgn_people.sp_person.last_name",
  69                                      "$sgn_people.sp_person.sp_person_id"],
  70                            sqlexpr=>"$sgn_people.sp_person.last_name || $sgn_people.sp_person.first_name
  71                                       || $sgn_people.sp_person.sp_person_id",
  72     );
  73
  74 __PACKAGE__->has_parameter(name   =>'status',
  75                            columns=>"$phenome.pub_curator.status",
  76                            );
  77 __PACKAGE__->has_parameter(name   =>'is_curated',
  78                            columns=>"$phenome.pub_curator.curated_by",
  79                            #sqlexpr=>"(count pub_curator.curated_by)",
  80                           # group  =>1,
  81                           # aggregate=>1,
  82     );
  83 __PACKAGE__->has_parameter(name   =>'date_stored',
  84                            columns=>["$phenome.pub_curator.date_stored"],
  85     );
  86
  87
  88 __PACKAGE__->has_complex_parameter( name => 'any_name',
  89                                     uses => [qw/ title series /],
  90                                     setter => sub {
  91                                         my ($self, @args) = @_;
  92                                         $self->title(@args);
  93                                         $self->series(@args);
  94
  95                                         $self->compound('&t OR &t' ,'title', 'series');
  96                                     }
  97     );
  98
  99 ###### NOW WWW STUFF ###
 100
 101 sub request_to_params {
 102     my($self, %params) = @_;
 103
 104     #sanitize all the parameters
 105     foreach my $key (keys %params) {
 106         if( $params{$key} ) {
 107             $params{$key} =~ s/[;\'\",]//g;
 108         }
 109     }
 110
 111     if($params{any_name}) {
 112         $self->any_name('ILIKE ?',"%$params{any_name}%");
 113     }
 114
 115     #if ($params{editor} =~ m/^\d/) {
 116 #       $self->editor('= ?', "$params{editor}");
 117     if ($params{assigned_to}) {
 118         $self->assigned_to('ILIKE ?', "%$params{assigned_to}%");
 119     }
 120
 121     if ($params{is_curated}) {
 122         $self->is_curated('IS NOT NULL');
 123     }
 124
 125     if ($params{author}) {
 126         $self->author('ILIKE ?', "%$params{author}%");
 127     }
 128     if ($params{date_stored}) {
 129         $self->date_stored('> ?', "$params{date_stored}");
 130     }
 131     if($params{status}) {
 132         $self->status('ILIKE ?', "$params{status}");
 133     }
 134
 135     #page number
 136     if( defined($params{page}) ) {
 137         $self->page($params{page});
 138     }
 139 }
 140
 141 sub _to_scalars {
 142     my $self= shift;
 143     my $search= shift;
 144     my %params;
 145
 146     no warnings 'uninitialized';
 147
 148     #this part defines the mapping from get/post data to search params
 149
 150     ($params{any_name}) = $self->param_bindvalues('any_name');
 151     $params{any_name} =~ s/%//g;
 152
 153     ($params{author}) = $self->param_bindvalues('author');
 154     $params{author} =~ s/%//g;
 155
 156     ($params{assigned_to}) = $self->param_bindvalues('assigned_to');
 157     $params{assigned_to} =~ s/%//g;
 158
 159     ($params{date_stored}) = $self->param_bindvalues('date_stored');
 160     $params{date_stored} =~ s/%//g;
 161
 162     ($params{status}) = $self->param_bindvalues('status');
 163
 164     $params{is_curated} = $self->pattern_match_parameter('is_curated',  /IS NOT NULL/);
 165
 166     return %params;
 167 }
 168
 169 sub to_html {
 170     my $self = shift;
 171     my $search = 'advanced';
 172     my %scalars = $self->_to_scalars($search);
 173
 174     #make %pname, a tied hash that uniqifies names the make_pname
 175     # function is in CXGN::Page::WebForm, which is a parent of
 176     # CXGN::Search::DBI::Simple::WWWQuery
 177     $self->make_pname;
 178     our %pname;
 179
 180     my $dbh=_cached_dbh();
 181
 182     my @stat_list= ("", "pending", "curated", "rejected", "no gene");
 183     my $stats = simple_selectbox_html( choices  => \@stat_list,
 184                                           name     => $pname{status},
 185                                           selected => $scalars{status},
 186                                           );
 187
 188     my $is_curated= $self->uniqify_name('is_curated');
 189     my $any_name = $self->uniqify_name('any_name');
 190     my $author = $self->uniqify_name('author');
 191     my $assigned_to = $self->uniqify_name('assigned_to');
 192     my $date_stored = $self->uniqify_name('date_stored');
 193
 194
 195     #check boxes
 196     @scalars{qw/ is_curated is_assigned /} =
 197         map {$_ ? 'checked="checked" ' : undef} @scalars{qw/ is_curated is_assigned /};
 198
 199     my $a_search=
 200         info_table_html(
 201                          'Title'=>qq|<input name="$pname{any_name}" value="$scalars{any_name}" size="60" />|,
 202                          __border =>0,) .
 203         info_table_html (
 204                          'Author' => qq|<input name = "$pname{author}" value="$scalars{author}" size="20" />|,
 205                          'Date stored' =>qq|<input name="$pname{date_stored}" value="$scalars{date_stored}" size="10"/>|,
 206                          'SGN curator'=> qq|<input name="$pname{assigned_to}" value="$scalars{assigned_to}" size="20" />|,
 207                          'Status' => $stats,
 208                          'Curated'    => qq|<input type="checkbox" name="$is_curated" $scalars{is_curated}  /><br />|,
 209                          __border   =>0,
 210                          __multicol =>2,
 211                          __tableattrs => 'width="100%"',
 212                          );
 213
 214     #$scalars{is_curated}   ||= '';
 215
 216     my $html_ret = <<EOHTML;
 217     <table><tr></tr>
 218         <tr><td>$a_search</td></tr>
 219     <tr><td><a href="/chado/publication.pl?action=new">[Submit new publication]</a> </td>
 220     </tr></table>
 221     <br />
 222         <div align="center"><input type="submit" value="Search"/></div>
 223 EOHTML
 224 }
 225
 226 sub quick_search {
 227     my ($self,$term) = @_;
 228     $self->any_name('ILIKE ?', "%$term%");
 229     return $self;
 230 }
 231
 232 ###
 233 1;#do not remove
 234 ###