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
  19 my $individuals_range_detail_page = CXGN::Phenome::IndividualsRangeDetailPage->new();
  20
  21 package CXGN::Phenome::IndividualsRangeDetailPage;
  22
  23
  24 use CXGN::Page;
  25 use CXGN::Page::FormattingHelpers qw /info_section_html
  26                                       page_title_html
  27                                       columnar_table_html
  28                                       html_optional_show
  29                                       info_table_html
  30                                       tooltipped_text
  31                                       html_alternate_show
  32                                       /;
  33
  34 use CXGN::Phenome::Population;
  35 use CXGN::Phenome::PopulationDbxref;
  36 use CXGN::Tools::WebImageCache;
  37 use CXGN::VHost;
  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 use 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         print STDERR "Generating EditableForm..\n";
 104         $form = CXGN::Page::Form::Editable->new();
 105     }
 106     else {
 107         print STDERR "Generating static Form...\n";
 108         $form = CXGN::Page::Form::Static->new();
 109     }
 110
 111    $form->add_label (
 112                       display_name=>"Name:",
 113                       field_name=>"name",
 114                       contents=> $pop_link,
 115                      );
 116
 117     $form->add_textarea(
 118                           display_name=>"Description: ",
 119                           field_name=>"description",
 120                           object=>$population,
 121                           getter=>"get_description", setter=>"set_description",
 122                           columns => 40,
 123                           rows =>4,
 124                           );
 125
 126
 127     $form->add_label( display_name=>"Uploaded by: ",
 128                           field_name=>"submitter",
 129                           contents=>$submitter_link,
 130                           );
 131     $form->add_hidden( field_name=>"population_id", contents=>$args{population_id});
 132
 133     $form->add_hidden (
 134                        field_name => "sp_person_id",
 135                        contents   =>$self->get_user()->get_sp_person_id(),
 136                        object     => $population,
 137                        setter     =>"set_sp_person_id",
 138                        );
 139
 140     $form->add_hidden( field_name=>"action", contents=>"store"  );
 141
 142
 143
 144
 145
 146     $self->set_form($form);
 147
 148     if ($self->get_action=~ /view|edit/) {
 149         $self->get_form->from_database();
 150
 151
 152     }elsif ($self->get_action=~ /store/) {
 153         $self->get_form->from_request($self->get_args());
 154
 155  }
 156
 157
 158
 159 }
 160
 161 sub display_page {
 162     my $self = shift;
 163
 164 $self->get_page->add_style( text => <<EOS);
 165 a.abstract_optional_show {
 166   color: blue;
 167   cursor: pointer;
 168   white-space: nowrap;
 169 }
 170 div.abstract_optional_show {
 171   background: #f0f0ff;
 172   border: 1px solid #9F9FC7;
 173   margin: 0.2em 1em 0.2em 1em;
 174   padding: 0.2em 0.5em 0.2em 1em;
 175 }
 176 EOS
 177
 178
 179
 180     my %args = $self->get_args();
 181     my $population = $self->get_object();
 182     my $population_id = $self->get_object_id();
 183     my $population_name = $population->get_name();
 184     my $login_user= $self->get_user();
 185     my $login_user_id= $login_user->get_sp_person_id();
 186     my $login_user_type= $login_user->get_user_type();
 187
 188
 189     $self->get_page()->header("SGN Population name: $population_name");
 190
 191     print page_title_html("SGN population: $population_name \n");
 192
 193     my $population_html .= $self->get_form()->as_table_string();
 194
 195     my $phenotype = "";
 196     my @phenotype;
 197
 198     my @cvterm_names;
 199
 200     my $cvterm_id = $args{cvterm_id};
 201     my $lower = $args{lower};
 202     my $upper = $args{upper};
 203
 204     my ($indl_id, $indl_name, $value)= $population->indls_range_cvterm($cvterm_id, $lower, $upper);
 205     my @indls_id = @$indl_id;
 206     my $indls_count = scalar @indls_id;
 207
 208
 209     my $cvterm = CXGN::Chado::Cvterm->new($self->get_dbh(), $args{cvterm_id});
 210     my $cvterm_name = $cvterm->get_cvterm_name();
 211     my $cvterm_id = $args{cvterm_id};
 212     my ($min, $max, $avg, $count)= $population->get_pop_data_summary($cvterm_id);
 213
 214             for (my $i=0; $i<@$indl_name; $i++) {
 215
 216         push  @phenotype,  [map {$_} ( qq | <a href="/phenome/individual.pl?individual_id=$indl_id->[$i]">$indl_name->[$i]</a>|, $value->[$i]) ];
 217     }
 218
 219
 220     my ($phenotype_data, $data_view, $data_download);
 221
 222     my $cvterm_note = " <br><b>$indls_count plant accessions had
 223                             $cvterm_name values >$lower but <= $upper.
 224                             The population average, minimum, and maximum
 225                             values for the trait were $avg, $min, and $max,
 226                             respectively.</b> <br />";
 227
 228     if (@phenotype) {
 229         $phenotype_data = columnar_table_html(headings => [
 230                                                            'Plant accession',
 231                                                            'Value',
 232
 233                                                            ],
 234                                               data     =>\@phenotype,
 235                                               __alt_freq   =>2,
 236                                               __alt_width  =>1,
 237                                               __alt_offset =>3,
 238                                               __align =>'l',
 239                                               );
 240
 241         $data_view = html_optional_show("phenotype",
 242                                         'View/hide phenotype data summary',
 243                                         qq|$phenotype_data</b>|,
 244                                         1, #<  show data by default
 245                                         );
 246         $data_download .=  qq { <span><a href="pop_download.pl?population_id=$population_id"><b>\[download population raw data\]</b></a></span> };
 247     }
 248
 249     my $page="../phenome/indls_range_cvterm.pl?cvterm_id=$cvterm_id&amp;lower=$lower&amp;upper=$upper&amp;population_id=$population_id ";
 250     $args{calling_page} = $page;
 251
 252
 253     my $pubmed;
 254     my $url_pubmed = qq | http://www.ncbi.nlm.nih.gov/pubmed/|;
 255
 256     my @publications = $population->get_population_publications();
 257     my $abstract_view;
 258     my $abstract_count = 0;
 259
 260
 261
 262     foreach my $pub (@publications) {
 263         my ($title, $abstract, $authors, $journal, $pyear, $volume, $issue, $pages, $obsolete, $pub_id, $accession);
 264         $abstract_count++;
 265
 266         my @dbxref_objs = $pub->get_dbxrefs();
 267         my $dbxref_obj = shift(@dbxref_objs);
 268
 269         $obsolete = $population->get_population_dbxref($dbxref_obj)->get_obsolete();
 270
 271         if ($obsolete eq 'f') {
 272         $pub_id = $pub->get_pub_id();
 273         $accession = $pub->get_accession();
 274         $title = $pub->get_title();
 275         $abstract = $pub->get_abstract();
 276         $pyear = $pub->get_pyear();
 277         $volume = $pub->get_volume();
 278         $journal = $pub->get_series_name();
 279         $pages = $pub->get_pages();
 280         $issue = $pub->get_issue();
 281         $accession = $dbxref_obj->get_accession();
 282         my $pub_info = qq|<a href="/chado/publication.pl?pub_id=$pub_id" >PMID:$accession</a> |;
 283         my @authors;
 284         my $authors;
 285         if ($pub_id) {
 286
 287            my @pubauthors_ids = $pub->get_pubauthors_ids($pub_id);
 288
 289            foreach my $pubauthor_id (@pubauthors_ids) {
 290                my  $pubauthor_obj = CXGN::Chado::Pubauthor->new($self->get_dbh, $pubauthor_id);
 291                my $last_name  = $pubauthor_obj->get_surname();
 292                my $first_names = $pubauthor_obj->get_givennames();
 293                my @first_names = split (/,/, $first_names);
 294                $first_names = shift (@first_names);
 295                push @authors, ("$first_names" ."  ". "$last_name");
 296                $authors = join (", ", @authors);
 297            }
 298        }
 299
 300
 301
 302
 303            $abstract_view = html_optional_show("abstracts$abstract_count",
 304                                'Show/hide abstract',
 305                                qq|$abstract <b> <i>$authors.</i> $journal. $pyear. $volume($issue). $pages.</b>|,
 306                                                  0, #< do not show by default
 307                                                  'abstract_optional_show', #< don't use the default button-like style
 308                                                 );
 309
 310
 311      $pubmed .= qq|<div><a href="$url_pubmed$accession" target="blank">$pub_info</a> $title $abstract_view </div> |;
 312     }
 313 }
 314
 315     print info_section_html(title   => 'Population details',
 316                             contents => $population_html,
 317                             );
 318
 319     print info_section_html(title   => 'Phenotype Data',
 320                             contents =>$cvterm_note . $data_view ." ".$data_download,
 321                             );
 322
 323
 324
 325     print info_section_html(title   => 'Literature annotation',
 326                             #subtitle => $pub_subtitle,
 327                             contents =>$pubmed ,
 328                             );
 329
 330
 331     if ($population_name) {
 332         my $page_comment_obj = CXGN::People::PageComment->new($self->get_dbh(), "population", $population_id);
 333         print $page_comment_obj->get_html();
 334     }
 335
 336
 337
 338     $self->get_page()->footer();
 339
 340
 341     exit();
 342 }
 343
 344
 345
 346
 347
 348