cgi-bin/phenome/population.pl

   1 use strict;
   2
   3 my $population_detail_page = CXGN::Phenome::PopulationDetailPage->new();
   4
   5 package CXGN::Phenome::PopulationDetailPage;
   6
   7
   8 use CXGN::Page;
   9 use CXGN::Page::FormattingHelpers qw /info_section_html
  10                                       page_title_html
  11                                       columnar_table_html
  12                                       html_optional_show
  13                                       info_table_html
  14                                       tooltipped_text
  15                                       html_alternate_show
  16                                       /;
  17
  18 use CXGN::Phenome::Population;
  19 use CXGN::Phenome::PopulationDbxref;
  20 use CXGN::People::PageComment;
  21 use CXGN::People::Person;
  22 use CXGN::Chado::Publication;
  23 use CXGN::Chado::Pubauthor;
  24
  25 use CXGN::Contact;
  26 use CXGN::Map;
  27
  28
  29 use base qw / CXGN::Page::Form::SimpleFormPage CXGN::Phenome::Main/;
  30
  31 sub new {
  32     my $class = shift;
  33     my $self = $class->SUPER::new(@_);
  34     $self->set_script_name("population.pl");
  35
  36
  37     return $self;
  38 }
  39
  40 sub define_object {
  41     my $self = shift;
  42
  43     # call set_object_id, set_object and set_primary_key here
  44     # with the appropriate parameters.
  45     #
  46     $self->set_dbh(CXGN::DB::Connection->new('phenome'));
  47     my %args = $self->get_args();
  48     my $population_id= $args{population_id};
  49     unless (!$population_id || $population_id =~m /^\d+$/) { $self->get_page->message_page("No population exists for identifier $population_id"); }
  50     $self->set_object_id($population_id);
  51     $self->set_object(CXGN::Phenome::Population->new($self->get_dbh(),$self->get_object_id()));
  52     $self->set_primary_key("population_id");
  53     $self->set_owners($self->get_object()->get_owners());
  54 }
  55
  56
  57
  58
  59 sub generate_form {
  60     my $self = shift;
  61
  62     $self->init_form();
  63
  64     my %args = $self->get_args();
  65
  66     my $population = $self->get_object();
  67     my $population_id = $self->get_object_id();
  68     my $type_id = $args{type_id};
  69     my $type=$args{type};
  70
  71     my ($submitter, $submitter_link) = $self->submitter();
  72
  73     my $login_user= $self->get_user();
  74     my $login_user_id= $login_user->get_sp_person_id();
  75     my $form = undef;
  76
  77     if ($self->get_action()=~/edit|store/ && ($login_user_id = $submitter || $self->get_user()->get_user_type() eq 'curator') ) {
  78         print STDERR "Generating EditableForm..\n";
  79         $form = CXGN::Page::Form::Editable->new();
  80     }
  81     else {
  82         print STDERR "Generating static Form...\n";
  83         $form = CXGN::Page::Form::Static->new();
  84     }
  85
  86    $form->add_field(
  87                       display_name=>"Name:",
  88                       field_name=>"name",
  89                       length=>15,
  90                       object=>$population,
  91                       getter=>"get_name",
  92                       setter=>"set_name",
  93                       validate => 'string',
  94                       );
  95     $form->add_textarea(
  96                           display_name=>"Description: ",
  97                           field_name=>"description",
  98                           object=>$population,
  99                           getter=>"get_description", setter=>"set_description",
 100                           columns => 40,
 101                           rows =>4,
 102                           );
 103
 104
 105     $form->add_label( display_name=>"Uploaded by: ",
 106                           field_name=>"submitter",
 107                           contents=>$submitter_link,
 108                           );
 109     $form->add_hidden( field_name=>"population_id", contents=>$args{population_id});
 110
 111     $form->add_hidden (
 112                        field_name => "sp_person_id",
 113                        contents   =>$self->get_user()->get_sp_person_id(),
 114                        object     => $population,
 115                        setter     =>"set_sp_person_id",
 116                        );
 117
 118     $form->add_hidden( field_name=>"action", contents=>"store"  );
 119
 120
 121
 122
 123
 124     $self->set_form($form);
 125
 126     if ($self->get_action=~ /view|edit/) {
 127         $self->get_form->from_database();
 128
 129
 130     }elsif ($self->get_action=~ /store/) {
 131         $self->get_form->from_request($self->get_args());
 132
 133  }
 134
 135
 136
 137 }
 138
 139 sub display_page {
 140     my $self = shift;
 141
 142     $self->get_page->add_style( text => <<EOS);
 143
 144 a.abstract_optional_show {
 145   color: blue;
 146   cursor: pointer;
 147   white-space: nowrap;
 148 }
 149 div.abstract_optional_show {
 150   background: #f0f0ff;
 151   border: 1px solid #9F9FC7;
 152   margin: 0.2em 1em 0.2em 1em;
 153   padding: 0.2em 0.5em 0.2em 1em;
 154 }
 155 EOS
 156
 157
 158
 159     my %args = $self->get_args();
 160
 161     my $population = $self->get_object();
 162     my $population_id = $self->get_object_id();
 163     my $population_name = $population->get_name();
 164
 165     my $action = $args{action};
 166     if (!$population_id && $action ne 'new' && $action ne 'store')
 167                      { $self->get_page->message_page("No population exists for this identifier"); }
 168
 169     #used to show certain elements to only the proper users
 170     my $login_user= $self->get_user();
 171     my $login_user_id= $login_user->get_sp_person_id();
 172     my $login_user_type= $login_user->get_user_type();
 173     my $page="../phenome/population.pl?population_id=$population_id";
 174
 175     $self->get_page()->header("SGN Population name: $population_name");
 176
 177     print page_title_html("Population: $population_name \n");
 178
 179     my $page="../phenome/population.pl?population_id=$population_id";
 180     $args{calling_page} = $page;
 181
 182     my $population_html = $self->get_edit_link_html(). "\t[<a href=/phenome/qtl_form.pl>New QTL Population</a>] <br />";
 183
 184     #print all editable form  fields
 185     $population_html .= $self->get_form()->as_table_string();
 186
 187
 188     my $phenotype = "";
 189     my @phenotype;
 190     my $graph_icon = qq |<img src="../documents/img/pop_graph.png"/> |;
 191
 192     if ($population->get_web_uploaded()) {
 193         my @traits = $population->get_cvterms();
 194
 195         foreach my $trait (@traits)  {
 196             my $trait_id = $trait->get_user_trait_id();
 197             my $trait_name = $trait->get_name();
 198             my $definition = $trait->get_definition();
 199             my ($min, $max, $avg, $std, $count)= $population->get_pop_data_summary($trait_id);
 200
 201             my $cvterm_obj  = CXGN::Chado::Cvterm::get_cvterm_by_name( $self->get_dbh(), $trait_name);
 202             my $trait_link;
 203             my $cvterm_id = $cvterm_obj->get_cvterm_id();
 204             if ($cvterm_id)
 205             {
 206
 207                 print STDERR "cvterm_id: $cvterm_id\n";
 208                 $trait_link = qq |<a href="/chado/cvterm.pl?cvterm_id=$cvterm_id">$trait_name</a>|;
 209
 210             } else
 211             {
 212                 print STDERR "trait_id: $trait_id\n";
 213                 $trait_link = qq |<a href="/phenome/trait.pl?trait_id=$trait_id">$trait_name</a>|;
 214             }
 215
 216
 217             if ($definition) {
 218                 push  @phenotype,  [map {$_} ( (tooltipped_text($trait_link, $definition)),
 219                                     $min, $max, $avg,
 220                            qq | <a href="/phenome/population_indls.pl?population_id=$population_id&amp;cvterm_id=$trait_id">
 221                                  $count</a>
 222                               |,
 223                            qq | <a href="/phenome/population_indls.pl?population_id=$population_id&amp;cvterm_id=$trait_id">
 224                                   $graph_icon</a>
 225                               | )];
 226             } else  { push  @phenotype,  [map {$_} ($trait_name, $min, $max, $avg,
 227                           qq | <a href="/phenome/population_indls.pl?population_id=$population_id&amp;cvterm_id=$trait_id">
 228                              $count</a>
 229                              |,
 230                            qq | <a href="/phenome/population_indls.pl?population_id=$population_id&amp;cvterm_id=$trait_id">
 231                                   $graph_icon</a>
 232                               |  )];
 233             }
 234         }
 235     }
 236      else {
 237          my @cvterms = $population->get_cvterms();
 238          foreach my $cvterm(@cvterms)  {
 239              my ($min, $max, $avg, $std, $count)= $population->get_pop_data_summary($cvterm->get_cvterm_id());
 240              my $cvterm_id = $cvterm->get_cvterm_id();
 241              my $cvterm_name = $cvterm->get_cvterm_name();
 242              if ($cvterm->get_definition()) {
 243                  push  @phenotype,  [map {$_} ( (tooltipped_text( qq|<a href="/chado/cvterm.pl?cvterm_id=$cvterm_id">
 244                                                                       $cvterm_name</a>
 245                                                                      |,
 246                                     $cvterm->get_definition())), $min, $max, $avg,
 247                           qq | <a href="/phenome/population_indls.pl?population_id=$population_id&amp;cvterm_id=$cvterm_id">
 248                              $count</a>
 249                              |,
 250                           qq | <a href="/phenome/population_indls.pl?population_id=$population_id&amp;cvterm_id=$cvterm_id">
 251                                $graph_icon</a>
 252                              | ) ];
 253              } else  { push  @phenotype,  [map {$_} (qq | <a href="/chado/cvterm.pl?cvterm_id=$cvterm_id">$cvterm_name</a>|,
 254                             $min, $max, $avg,
 255                      qq | <a href="/phenome/population_indls.pl?population_id=$population_id&amp;cvterm_id=$cvterm_id">
 256                           $count</a>
 257                         |,
 258                      qq | <a href="/phenome/population_indls.pl?population_id=$population_id&amp;cvterm_id=$cvterm_id">
 259                           $graph_icon</a>
 260                         |  ) ];
 261              }
 262          }
 263      }
 264
 265     my $accessions_link = qq |<a href="../search/phenotype_search.pl?wee9_population_id=$population_id">
 266                               See all accessions ...</a>
 267                              |;
 268
 269     my ($phenotype_data, $data_view, $data_download);
 270
 271     if (@phenotype) {
 272         $phenotype_data = columnar_table_html(headings => [
 273                                                            'Trait',
 274                                                            'Minimum',
 275                                                            'Maximum',
 276                                                            'Average',
 277                                                            'No. of lines',
 278                                                            'QTL(s)...',
 279                                                            ],
 280                                               data     =>\@phenotype,
 281                                               __alt_freq   =>2,
 282                                               __alt_width  =>1,
 283                                               __alt_offset =>3,
 284                                               __align =>'l',
 285                                               );
 286
 287 #       $data_view = html_optional_show("phenotype",
 288 #                                       'View/hide phenotype data summary',
 289 #                                       qq|$phenotype_data</b>|,
 290 #                                       1, #<  show data by default
 291 #                                       );
 292
 293         $data_download .=  qq { <span><br/><br/>Download:<a href="pop_download.pl?population_id=$population_id"><b>\
 294                                 [Phenotype raw data]</b></a><a href="genotype_download.pl?population_id=$population_id">\
 295                                 <b>[Genotype raw data\]</b></a></span>
 296                               };
 297     }
 298
 299
 300     my $pub_subtitle;
 301     if ($population_name && ($login_user_type eq 'curator' || $login_user_type eq 'submitter')) {
 302         $pub_subtitle .= qq|<a href="../chado/add_publication.pl?type=population&amp;type_id=$population_id&amp;refering_page=$page&amp;action=new">[Associate publication]</a>|;
 303
 304     }
 305
 306     else { $pub_subtitle= qq|<span class=\"ghosted\">[Associate publication]</span>|;
 307
 308     }
 309
 310
 311     my $pubmed;
 312     my $url_pubmed = qq | http://www.ncbi.nlm.nih.gov/pubmed/|;
 313
 314     my @publications = $population->get_population_publications();
 315     my $abstract_view;
 316     my $abstract_count = 0;
 317
 318
 319
 320     foreach my $pub (@publications) {
 321         my ($title, $abstract, $authors, $journal, $pyear,
 322             $volume, $issue, $pages, $obsolete, $pub_id, $accession
 323            );
 324         $abstract_count++;
 325
 326         my @dbxref_objs = $pub->get_dbxrefs();
 327         my $dbxref_obj = shift(@dbxref_objs);
 328
 329         $obsolete = $population->get_population_dbxref($dbxref_obj)->get_obsolete();
 330
 331         if ($obsolete eq 'f') {
 332             $pub_id = $pub->get_pub_id();
 333             $title = $pub->get_title();
 334             $abstract = $pub->get_abstract();
 335             $pyear = $pub->get_pyear();
 336             $volume = $pub->get_volume();
 337             $journal = $pub->get_series_name();
 338             $pages = $pub->get_pages();
 339             $issue = $pub->get_issue();
 340
 341             $accession = $dbxref_obj->get_accession();
 342             my $pub_info = qq|<a href="/chado/publication.pl?pub_id=$pub_id" >PMID:$accession</a>|;
 343
 344             my @authors;
 345             my $authors;
 346             if ($pub_id) {
 347
 348                 my @pubauthors_ids = $pub->get_pubauthors_ids($pub_id);
 349
 350                 foreach my $pubauthor_id (@pubauthors_ids) {
 351                     my  $pubauthor_obj = CXGN::Chado::Pubauthor->new($self->get_dbh, $pubauthor_id);
 352                     my $last_name  = $pubauthor_obj->get_surname();
 353                     my $first_names = $pubauthor_obj->get_givennames();
 354                     my @first_names = split (/,/, $first_names);
 355                     $first_names = shift (@first_names);
 356                     push @authors, ("$first_names" ."  ". "$last_name");
 357                     $authors = join (", ", @authors);
 358                 }
 359             }
 360
 361
 362
 363
 364             $abstract_view = html_optional_show("abstracts$abstract_count",
 365                                'Show/hide abstract',
 366                                qq|$abstract <b> <i>$authors.</i> $journal. $pyear. $volume($issue). $pages.</b>|,
 367                                                  0, #< do not show by default
 368                                                  'abstract_optional_show', #< don't use the default button-like style
 369                                                 );
 370
 371
 372             $pubmed .= qq| <div><a href="$url_pubmed$accession" target="blank">$pub_info</a> $title $abstract_view</div> |;
 373         }
 374     }
 375
 376     my $is_public = $population->get_privacy_status();
 377     my ($submitter_obj, $submitter_link) = $self->submitter();
 378     my $map_link = $self->genetic_map();
 379     print info_section_html(title   => 'Population Details',
 380                             contents => $population_html,
 381                             );
 382
 383     if ($is_public ||
 384         $login_user_type eq 'curator' ||
 385         $login_user_id ==
 386         $population->get_sp_person_id()
 387        )  {
 388         if ($phenotype_data) {
 389             print info_section_html(title    => 'Phenotype Data and QTLs',
 390                                     contents => $phenotype_data ." ".$data_download
 391                                    );
 392         } else {
 393             print info_section_html(title    => 'Phenotype Data',
 394                                     contents => $accessions_link
 395                                    );
 396         }
 397
 398         unless (!$map_link) {
 399             print info_section_html( title    => 'Genetic Map',
 400                                      contents => $map_link
 401                                    );
 402         }
 403
 404     } else {
 405         my $message = "The QTL data for this population is not public yet.
 406                        If you would like to know more about this data,
 407                        please contact the owner of the data: <b>$submitter_link</b>
 408                        or email to SGN:
 409                        <a href=mailto:sgn-feedback\@sgn.cornell.edu>
 410                        sgn-feedback\@sgn.cornell.edu</a>.\n";
 411
 412         print info_section_html(title   => 'Phenotype Data and QTLs',
 413                                 contents =>$message,
 414                                );
 415
 416     }
 417     print info_section_html(title   => 'Literature Annotation',
 418                             #subtitle => $pub_subtitle,
 419                             contents => $pubmed,
 420                             );
 421
 422     if ($population_name) {
 423         # change sgn_people.forum_topic.page_type and the CHECK constraint!!
 424         my $page_comment_obj = CXGN::People::PageComment->new($self->get_dbh(), "population", $population_id);
 425         print $page_comment_obj->get_html();
 426     }
 427
 428     $self->get_page()->footer();
 429
 430
 431     exit();
 432 }
 433
 434
 435
 436
 437
 438
 439 # override store to check if a locus with the submitted symbol/name already exists in the database
 440
 441 sub store {
 442    my $self = shift;
 443    my $population = $self->get_object();
 444    my $population_id = $self->get_object_id();
 445    my %args = $self->get_args();
 446
 447    $self->SUPER::store(0);
 448
 449  exit();
 450 }
 451
 452
 453 sub submitter {
 454     my $self = shift;
 455     my $population = $self->get_object();
 456     my $sp_person_id= $population->get_sp_person_id();
 457     my $submitter = CXGN::People::Person->new($self->get_dbh(), $population->get_sp_person_id());
 458     my $submitter_name = $submitter->get_first_name()." ".$submitter->get_last_name();
 459     my $submitter_link = qq |<a href="/solpeople/personal-info.pl?sp_person_id=$sp_person_id">$submitter_name</a> |;
 460
 461     return $submitter, $submitter_link;
 462
 463 }
 464
 465 sub genetic_map {
 466     my $self     = shift;
 467     my $mapv_id  = $self->get_object()->mapversion_id();
 468
 469     if ($mapv_id) {
 470         my $map      = CXGN::Map->new( $self->get_dbh(), { map_version_id => $mapv_id } );
 471         my $map_name = $map->get_long_name();
 472         my $genetic_map =
 473             qq | <a href=/cview/map.pl?map_version_id=$mapv_id>$map_name</a>|;
 474
 475         return $genetic_map;
 476     }
 477     else {
 478         return;
 479     }
 480
 481 }
 482
 483
 484