cgi-bin/phenome/indls_range_cvterm.pl

   1 #!/usr/bin/perl -wT
   2
   3 =head1 DESCRIPTION
   4
   5 generates a page with the list of individual
   6 plant accessions (and their corresponding trait values)
   7 falling within a phenotypic range in a population.
   8
   9 =head1 AUTHOR
  10
  11 Isaak Y Tecle (iyt2@cornell.edu)
  12
  13 =cut
  14
  15
  16
  17 use strict;
  18 use warnings;
  19
  20 my $individuals_range_detail_page = CXGN::Phenome::IndividualsRangeDetailPage->new();
  21
  22 package CXGN::Phenome::IndividualsRangeDetailPage;
  23
  24
  25 use CXGN::Page;
  26 use CXGN::Page::FormattingHelpers qw /info_section_html
  27                                       page_title_html
  28                                       columnar_table_html
  29                                       html_optional_show
  30                                       info_table_html
  31                                       tooltipped_text
  32                                       html_alternate_show
  33                                       /;
  34
  35 use CXGN::Phenome::Population;
  36 use CXGN::Phenome::PopulationDbxref;
  37 use CXGN::Tools::WebImageCache;
  38 use CXGN::People::PageComment;
  39 use CXGN::People::Person;
  40 use CXGN::Chado::Publication;
  41 use CXGN::Chado::Pubauthor;
  42 use GD;
  43 #use GD::Image;
  44 use GD::Graph::bars;
  45 #BEGIN { local $SIG{__WARN__} = sub {}; require GD::Graph::Map }
  46 use Statistics::Descriptive;
  47 use CXGN::Scrap::AjaxPage;
  48 use CXGN::Contact;
  49
  50
  51
  52 use base qw / CXGN::Page::Form::SimpleFormPage CXGN::Phenome::Main/;
  53
  54 sub new {
  55     my $class = shift;
  56     my $self = $class->SUPER::new(@_);
  57     $self->set_script_name("indls_range_cvterm.pl");
  58
  59
  60     return $self;
  61 }
  62
  63 sub define_object {
  64     my $self = shift;
  65
  66     $self->set_dbh(CXGN::DB::Connection->new('phenome'));
  67     my %args = $self->get_args();
  68     my $population_id= $args{population_id};
  69     unless (!$population_id || $population_id =~m /^\d+$/) { $self->get_page->message_page("No population exists for identifier $population_id"); }
  70     $self->set_object_id($population_id);
  71     $self->set_object(CXGN::Phenome::Population->new($self->get_dbh(),$self->get_object_id()));
  72     $self->set_primary_key("population_id");
  73     $self->set_owners($self->get_object()->get_owners());
  74 }
  75
  76
  77
  78
  79 sub generate_form {
  80     my $self = shift;
  81
  82     $self->init_form();
  83
  84     my %args = $self->get_args();
  85
  86     my $population = $self->get_object();
  87     my $population_id = $self->get_object_id();
  88     my $type_id = $args{type_id};
  89     my $type=$args{type};
  90     my $pop_name = $population->get_name();
  91     my $pop_link = qq |<a href="/phenome/population.pl?population_id=$population_id">$pop_name</a> |;
  92
  93     my $sp_person_id= $population->get_sp_person_id();
  94     my $submitter = CXGN::People::Person->new($self->get_dbh(), $population->get_sp_person_id());
  95     my $submitter_name = $submitter->get_first_name()." ".$submitter->get_last_name();
  96     my $submitter_link = qq |<a href="/solpeople/personal-info.pl?sp_person_id=$sp_person_id">$submitter_name </a> |;
  97
  98
  99     my $login_user= $self->get_user();
 100     my $login_user_id= $login_user->get_sp_person_id();
 101     my $form = undef;
 102     if ($self->get_action()=~/edit|store/ && ($login_user_id = $submitter || $self->get_user()->get_user_type() eq 'curator') ) {
 103         $form = CXGN::Page::Form::Editable->new();
 104     }
 105     else {
 106         $form = CXGN::Page::Form::Static->new();
 107     }
 108
 109    $form->add_label (
 110                       display_name=>"Name:",
 111                       field_name=>"name",
 112                       contents=> $pop_link,
 113                      );
 114
 115     $form->add_textarea(
 116                           display_name=>"Description: ",
 117                           field_name=>"description",
 118                           object=>$population,
 119                           getter=>"get_description", setter=>"set_description",
 120                           columns => 40,
 121                           rows =>4,
 122                           );
 123
 124
 125     $form->add_label( display_name=>"Uploaded by: ",
 126                           field_name=>"submitter",
 127                           contents=>$submitter_link,
 128                           );
 129     $form->add_hidden( field_name=>"population_id", contents=>$args{population_id});
 130
 131     $form->add_hidden (
 132                        field_name => "sp_person_id",
 133                        contents   =>$self->get_user()->get_sp_person_id(),
 134                        object     => $population,
 135                        setter     =>"set_sp_person_id",
 136                        );
 137
 138     $form->add_hidden( field_name=>"action", contents=>"store"  );
 139
 140
 141
 142
 143
 144     $self->set_form($form);
 145
 146     if ($self->get_action=~ /view|edit/) {
 147         $self->get_form->from_database();
 148
 149
 150     }elsif ($self->get_action=~ /store/) {
 151         $self->get_form->from_request($self->get_args());
 152
 153  }
 154
 155
 156
 157 }
 158
 159 sub display_page {
 160     my $self = shift;
 161
 162 $self->get_page->add_style( text => <<EOS);
 163 a.abstract_optional_show {
 164   color: blue;
 165   cursor: pointer;
 166   white-space: nowrap;
 167 }
 168 div.abstract_optional_show {
 169   background: #f0f0ff;
 170   border: 1px solid #9F9FC7;
 171   margin: 0.2em 1em 0.2em 1em;
 172   padding: 0.2em 0.5em 0.2em 1em;
 173 }
 174 EOS
 175
 176
 177
 178     my %args = $self->get_args();
 179     my $population = $self->get_object();
 180     my $population_id = $self->get_object_id();
 181     my $population_name = $population->get_name();
 182     my $login_user= $self->get_user();
 183     my $login_user_id= $login_user->get_sp_person_id();
 184     my $login_user_type= $login_user->get_user_type();
 185
 186
 187     $self->get_page()->header("SGN Population name: $population_name");
 188
 189     print page_title_html("SGN population: $population_name \n");
 190
 191     my $population_html .= $self->get_form()->as_table_string();
 192
 193     my $phenotype = "";
 194     my @phenotype;
 195
 196     my @cvterm_names;
 197
 198     my $cvterm_id = $args{cvterm_id};
 199     my $lower = $args{lower};
 200     my $upper = $args{upper};
 201
 202     my ($indl_id, $indl_name, $value)= $population->indls_range_cvterm($cvterm_id, $lower, $upper);
 203     my @indls_id = @$indl_id;
 204     my $indls_count = scalar @indls_id;
 205
 206
 207     my $cvterm = CXGN::Chado::Cvterm->new($self->get_dbh(), $args{cvterm_id});
 208     my $cvterm_name = $cvterm->get_cvterm_name();
 209     $cvterm_id = $args{cvterm_id};
 210     my ($min, $max, $avg, $count)= $population->get_pop_data_summary($cvterm_id);
 211
 212             for (my $i=0; $i<@$indl_name; $i++) {
 213
 214         push  @phenotype,  [map {$_} ( qq | <a href="/phenome/individual.pl?individual_id=$indl_id->[$i]">$indl_name->[$i]</a>|, $value->[$i]) ];
 215     }
 216
 217
 218     my ($phenotype_data, $data_view, $data_download);
 219
 220     my $cvterm_note = " <br><b>$indls_count plant accessions had
 221                             $cvterm_name values >$lower but <= $upper.
 222                             The population average, minimum, and maximum
 223                             values for the trait were $avg, $min, and $max,
 224                             respectively.</b> <br />";
 225
 226     if (@phenotype) {
 227         $phenotype_data = columnar_table_html(headings => [
 228                                                            'Plant accession',
 229                                                            'Value',
 230
 231                                                            ],
 232                                               data     =>\@phenotype,
 233                                               __alt_freq   =>2,
 234                                               __alt_width  =>1,
 235                                               __alt_offset =>3,
 236                                               __align =>'l',
 237                                               );
 238
 239         $data_view = html_optional_show("phenotype",
 240                                         'View/hide phenotype data summary',
 241                                         qq|<b>$phenotype_data</b>|,
 242                                         1, #<  show data by default
 243                                         );
 244         $data_download .=  qq { <span><a href="/qtl/download/phenotype/$population_id"><b>\[download population raw data\]</b></a></span> };
 245     }
 246
 247     my $page="../phenome/indls_range_cvterm.pl?cvterm_id=$cvterm_id&amp;lower=$lower&amp;upper=$upper&amp;population_id=$population_id ";
 248     $args{calling_page} = $page;
 249
 250
 251     my $pubmed;
 252     my $url_pubmed = qq | http://www.ncbi.nlm.nih.gov/pubmed/|;
 253
 254     my @publications = $population->get_population_publications();
 255     my $abstract_view;
 256     my $abstract_count = 0;
 257
 258
 259
 260     foreach my $pub (@publications) {
 261         my ($title, $abstract, $authors, $journal, $pyear, $volume, $issue, $pages, $obsolete, $pub_id, $accession);
 262         $abstract_count++;
 263
 264         my @dbxref_objs = $pub->get_dbxrefs();
 265         my $dbxref_obj = shift(@dbxref_objs);
 266
 267         $obsolete = $population->get_population_dbxref($dbxref_obj)->get_obsolete();
 268
 269         if ($obsolete eq 'f') {
 270         $pub_id = $pub->get_pub_id();
 271         $accession = $pub->get_accession();
 272         $title = $pub->get_title();
 273         $abstract = $pub->get_abstract();
 274         $pyear = $pub->get_pyear();
 275         $volume = $pub->get_volume();
 276         $journal = $pub->get_series_name();
 277         $pages = $pub->get_pages();
 278         $issue = $pub->get_issue();
 279         $accession = $dbxref_obj->get_accession();
 280         my $pub_info = qq|<a href="/publication/$pub_id/view" >PMID:$accession</a> |;
 281         my @authors;
 282         my $authors;
 283         if ($pub_id) {
 284
 285            my @pubauthors_ids = $pub->get_pubauthors_ids($pub_id);
 286
 287            foreach my $pubauthor_id (@pubauthors_ids) {
 288                my  $pubauthor_obj = CXGN::Chado::Pubauthor->new($self->get_dbh, $pubauthor_id);
 289                my $last_name  = $pubauthor_obj->get_surname();
 290                my $first_names = $pubauthor_obj->get_givennames();
 291                my @first_names = split (/,/, $first_names);
 292                $first_names = shift (@first_names);
 293                push @authors, ("$first_names" ."  ". "$last_name");
 294                $authors = join (", ", @authors);
 295            }
 296        }
 297
 298
 299
 300
 301            $abstract_view = html_optional_show("abstracts$abstract_count",
 302                                'Show/hide abstract',
 303                                qq|$abstract <b> <i>$authors.</i> $journal. $pyear. $volume($issue). $pages.</b>|,
 304                                                  0, #< do not show by default
 305                                                  'abstract_optional_show', #< don't use the default button-like style
 306                                                 );
 307
 308
 309      $pubmed .= qq|<div><a href="$url_pubmed$accession" target="blank">$pub_info</a> $title $abstract_view </div> |;
 310     }
 311 }
 312
 313     print info_section_html(title   => 'Population details',
 314                             contents => $population_html,
 315                             );
 316
 317     print info_section_html(title   => 'Phenotype Data',
 318                             contents =>$cvterm_note . $data_view ." ".$data_download,
 319                             );
 320
 321
 322
 323     print info_section_html(title   => 'Literature annotation',
 324                             #subtitle => $pub_subtitle,
 325                             contents =>$pubmed ,
 326                             );
 327
 328
 329     if ($population_name) {
 330         my $page_comment_obj = CXGN::People::PageComment->new($self->get_dbh(), "population", $population_id, $self->get_page()->{request}->uri()."?".$self->get_page()->{request}->args());
 331         print $page_comment_obj->get_html();
 332     }
 333
 334
 335
 336     $self->get_page()->footer();
 337
 338
 339     exit();
 340 }
 341
 342
 343
 344
 345
 346