cgi-bin/phenome/population.pl

   1 use strict;
   2 use warnings;
   3
   4 my $population_detail_page = CXGN::Phenome::PopulationDetailPage->new();
   5
   6 package CXGN::Phenome::PopulationDetailPage;
   7
   8
   9 use CXGN::Page;
  10 use CXGN::Page::FormattingHelpers qw /info_section_html
  11                                       page_title_html
  12                                       columnar_table_html
  13                                       html_optional_show
  14                                       info_table_html
  15                                       tooltipped_text
  16                                       html_alternate_show
  17                                       /;
  18
  19 use CXGN::Phenome::Population;
  20 use CXGN::Phenome::PopulationDbxref;
  21 use CXGN::People::PageComment;
  22 use CXGN::People::Person;
  23 use CXGN::Chado::Publication;
  24 use CXGN::Chado::Pubauthor;
  25
  26 use CXGN::Contact;
  27 use CXGN::Map;
  28
  29
  30 use base qw / CXGN::Page::Form::SimpleFormPage CXGN::Phenome::Main/;
  31
  32 sub new {
  33     my $class = shift;
  34     my $self = $class->SUPER::new(@_);
  35     $self->set_script_name("population.pl");
  36
  37
  38     return $self;
  39 }
  40
  41 sub define_object {
  42     my $self = shift;
  43
  44     # call set_object_id, set_object and set_primary_key here
  45     # with the appropriate parameters.
  46     #
  47     $self->set_dbh(CXGN::DB::Connection->new('phenome'));
  48     my %args = $self->get_args();
  49     my $population_id= $args{population_id};
  50     unless (!$population_id || $population_id =~m /^\d+$/) { $self->get_page->message_page("No population exists for identifier $population_id"); }
  51     $self->set_object_id($population_id);
  52     $self->set_object(CXGN::Phenome::Population->new($self->get_dbh(),$self->get_object_id()));
  53     $self->set_primary_key("population_id");
  54     $self->set_owners($self->get_object()->get_owners());
  55 }
  56
  57
  58
  59
  60 sub generate_form {
  61     my $self = shift;
  62
  63     $self->init_form();
  64
  65     my %args = $self->get_args();
  66
  67     my $population = $self->get_object();
  68     my $population_id = $self->get_object_id();
  69     my $type_id = $args{type_id};
  70     my $type=$args{type};
  71
  72     my ($submitter, $submitter_link) = $self->submitter();
  73
  74     my $login_user= $self->get_user();
  75     my $login_user_id= $login_user->get_sp_person_id();
  76     my $form = undef;
  77
  78     if ($self->get_action()=~/edit|store/ && ($login_user_id = $submitter || $self->get_user()->get_user_type() eq 'curator') ) {
  79         $form = CXGN::Page::Form::Editable->new();
  80     }
  81     else {
  82         $form = CXGN::Page::Form::Static->new();
  83     }
  84
  85    $form->add_field(
  86                       display_name=>"Name:",
  87                       field_name=>"name",
  88                       length=>15,
  89                       object=>$population,
  90                       getter=>"get_name",
  91                       setter=>"set_name",
  92                       validate => 'string',
  93                       );
  94     $form->add_textarea(
  95                           display_name=>"Description: ",
  96                           field_name=>"description",
  97                           object=>$population,
  98                           getter=>"get_description", setter=>"set_description",
  99                           columns => 40,
 100                           rows =>4,
 101                           );
 102
 103
 104     $form->add_label( display_name=>"Uploaded by: ",
 105                           field_name=>"submitter",
 106                           contents=>$submitter_link,
 107                           );
 108     $form->add_hidden( field_name=>"population_id", contents=>$args{population_id});
 109
 110     $form->add_hidden (
 111                        field_name => "sp_person_id",
 112                        contents   =>$self->get_user()->get_sp_person_id(),
 113                        object     => $population,
 114                        setter     =>"set_sp_person_id",
 115                        );
 116
 117     $form->add_hidden( field_name=>"action", contents=>"store"  );
 118
 119
 120
 121
 122
 123     $self->set_form($form);
 124
 125     if ($self->get_action=~ /view|edit/) {
 126         $self->get_form->from_database();
 127
 128
 129     }elsif ($self->get_action=~ /store/) {
 130         $self->get_form->from_request($self->get_args());
 131
 132  }
 133
 134
 135
 136 }
 137
 138 sub display_page {
 139     my $self = shift;
 140
 141     $self->get_page->add_style( text => <<EOS);
 142
 143 a.abstract_optional_show {
 144   color: blue;
 145   cursor: pointer;
 146   white-space: nowrap;
 147 }
 148 div.abstract_optional_show {
 149   background: #f0f0ff;
 150   border: 1px solid #9F9FC7;
 151   margin: 0.2em 1em 0.2em 1em;
 152   padding: 0.2em 0.5em 0.2em 1em;
 153 }
 154 EOS
 155
 156
 157
 158     my %args = $self->get_args();
 159
 160     my $population = $self->get_object();
 161     my $population_id = $self->get_object_id();
 162     my $population_name = $population->get_name();
 163
 164     my $action = $args{action};
 165     if (!$population_id && $action ne 'new' && $action ne 'store')
 166                      { $self->get_page->message_page("No population exists for this identifier"); }
 167
 168     #used to show certain elements to only the proper users
 169     my $login_user= $self->get_user();
 170     my $login_user_id= $login_user->get_sp_person_id();
 171     my $login_user_type= $login_user->get_user_type();
 172     my $page="../phenome/population.pl?population_id=$population_id";
 173
 174     $self->get_page()->header("SGN Population name: $population_name");
 175
 176     print page_title_html("Population: $population_name \n");
 177
 178     $args{calling_page} = $page;
 179
 180     my $population_html = $self->get_edit_link_html(). "\t[<a href=/phenome/qtl_form.pl>New QTL Population</a>] <br />";
 181
 182     #print all editable form  fields
 183     $population_html .= $self->get_form()->as_table_string();
 184
 185
 186     my ($phenotype, $is_qtl_pop);
 187     my @phenotype;
 188     my $graph_icon = qq |<img src="../documents/img/pop_graph.png"/> |;
 189
 190     my $qtltool = CXGN::Phenome::Qtl::Tools->new();
 191     my @pops = $qtltool->has_qtl_data();
 192
 193     foreach my $pops (@pops)
 194     {
 195         my $pops_id = $pops->get_population_id();
 196         if ($pops_id == $population_id)
 197         {
 198             $is_qtl_pop = 1;
 199         }
 200     }
 201
 202     if ($population->get_web_uploaded()) {
 203         my @traits = $population->get_cvterms();
 204
 205         foreach my $trait (@traits)  {
 206             my $trait_id = $trait->get_user_trait_id();
 207             my $trait_name = $trait->get_name();
 208             my $definition = $trait->get_definition();
 209             my ($min, $max, $avg, $std, $count)= $population->get_pop_data_summary($trait_id);
 210
 211             my $cvterm_obj  = CXGN::Chado::Cvterm::get_cvterm_by_name( $self->get_dbh(), $trait_name);
 212             my $trait_link;
 213             my $cvterm_id = $cvterm_obj->get_cvterm_id();
 214             if ($cvterm_id)
 215             {
 216                 $trait_link = qq |<a href="/chado/cvterm.pl?cvterm_id=$cvterm_id">$trait_name</a>|;
 217
 218             } else
 219             {
 220                 $trait_link = qq |<a href="/phenome/trait.pl?trait_id=$trait_id">$trait_name</a>|;
 221             }
 222
 223             if ($is_qtl_pop)
 224             {
 225                 if ($definition)
 226                 {
 227                     push  @phenotype,  [map {$_} ( (tooltipped_text($trait_link, $definition)),
 228                                     $min, $max, $avg,
 229                            qq | <a href="/phenome/population_indls.pl?population_id=$population_id&amp;cvterm_id=$trait_id">
 230                                  $count</a>
 231                               |,
 232                            qq | <a href="/phenome/population_indls.pl?population_id=$population_id&amp;cvterm_id=$trait_id">
 233                                   $graph_icon</a>
 234                               | )];
 235                 } else
 236                 {
 237                     push  @phenotype,  [map {$_} ($trait_name, $min, $max, $avg,
 238                           qq | <a href="/phenome/population_indls.pl?population_id=$population_id&amp;cvterm_id=$trait_id">
 239                              $count</a>
 240                              |,
 241                            qq | <a href="/phenome/population_indls.pl?population_id=$population_id&amp;cvterm_id=$trait_id">
 242                                   $graph_icon</a>
 243                               |  )];
 244                 }
 245             } else
 246             {
 247                 if ($definition)
 248                 {
 249                     push  @phenotype,  [map {$_} ( (tooltipped_text( $trait_link, $definition )),
 250                                     $min, $max, $avg, $count )];
 251                 } else
 252                 { push  @phenotype,  [map {$_} ( $trait_name, $min, $max, $avg, $count )];
 253                 }
 254             }
 255         }
 256     }
 257      else {
 258          my @cvterms = $population->get_cvterms();
 259          foreach my $cvterm(@cvterms)
 260          {
 261              my ($min, $max, $avg, $std, $count)= $population->get_pop_data_summary($cvterm->get_cvterm_id());
 262              my $cvterm_id = $cvterm->get_cvterm_id();
 263              my $cvterm_name = $cvterm->get_cvterm_name();
 264
 265              if ($is_qtl_pop)
 266              {
 267                  if ($cvterm->get_definition())
 268                  {
 269                      push  @phenotype,  [map {$_} ( (tooltipped_text( qq|<a href="/chado/cvterm.pl?cvterm_id=$cvterm_id">
 270                                                                       $cvterm_name</a>
 271                                                                      |,
 272                                     $cvterm->get_definition())), $min, $max, $avg, $count,
 273                           qq | <a href="/phenome/population_indls.pl?population_id=$population_id&amp;cvterm_id=$cvterm_id">
 274                                $graph_icon</a>
 275                              | ) ];
 276                  } else
 277                  { push  @phenotype,  [map {$_} (qq | <a href="/chado/cvterm.pl?cvterm_id=$cvterm_id">$cvterm_name</a>|,
 278                             $min, $max, $avg, $count,
 279                      qq | <a href="/phenome/population_indls.pl?population_id=$population_id&amp;cvterm_id=$cvterm_id">
 280                           $graph_icon</a>
 281                         |  ) ];
 282                  }
 283              } else
 284              {
 285                  if ($cvterm->get_definition())
 286                  {
 287                      push  @phenotype,  [map {$_} ( (tooltipped_text( qq|<a href="/chado/cvterm.pl?cvterm_id=$cvterm_id">
 288                                                                       $cvterm_name</a>
 289                                                                      |,
 290                                     $cvterm->get_definition())), $min, $max, $avg, $count) ];
 291                  } else
 292                  {
 293                      push  @phenotype,  [map {$_} (qq | <a href="/chado/cvterm.pl?cvterm_id=$cvterm_id">$cvterm_name</a>|,
 294                             $min, $max, $avg, $count ) ];
 295                  }
 296              }
 297          }
 298      }
 299
 300     my $accessions_link = qq |<a href="../search/phenotype_search.pl?wee9_population_id=$population_id">
 301                               See all accessions ...</a>
 302                              |;
 303
 304     my ($phenotype_data, $data_view, $data_download);
 305
 306     if (@phenotype)
 307     {
 308         if ($is_qtl_pop) {
 309             $phenotype_data = columnar_table_html(headings => [
 310                                                            'Trait',
 311                                                            'Minimum',
 312                                                            'Maximum',
 313                                                            'Average',
 314                                                            'No. of lines',
 315                                                            'QTL(s)...',
 316                                                            ],
 317                                               data     =>\@phenotype,
 318                                               __alt_freq   =>2,
 319                                               __alt_width  =>1,
 320                                               __alt_offset =>3,
 321                                               __align =>'l',
 322                                               );
 323
 324             $data_download .=  qq { <span><br/><br/>Download:<a href="pop_download.pl?population_id=$population_id"><b>\
 325                                 [Phenotype raw data]</b></a> <a href="genotype_download.pl?population_id=$population_id"><b>\
 326                                 [Genotype raw data]</b></a></span>
 327                               };
 328
 329
 330         } else
 331         {
 332             $phenotype_data = columnar_table_html(headings => [
 333                                                            'Trait',
 334                                                            'Minimum',
 335                                                            'Maximum',
 336                                                            'Average',
 337                                                            'No. of lines',
 338                                                            ],
 339                                               data     =>\@phenotype,
 340                                               __alt_freq   =>2,
 341                                               __alt_width  =>1,
 342                                               __alt_offset =>3,
 343                                               __align =>'l',
 344                                               );
 345
 346             $data_download .=  qq { <span><br/><br/>Download:<a href="pop_download.pl?population_id=$population_id"><b>\
 347                                 [Phenotype raw data]</b></a></span>
 348                               };
 349
 350         }
 351
 352
 353
 354     }
 355
 356
 357     my $pub_subtitle;
 358     if ($population_name && ($login_user_type eq 'curator' || $login_user_type eq 'submitter')) {
 359         $pub_subtitle .= qq|<a href="../chado/add_publication.pl?type=population&amp;type_id=$population_id&amp;refering_page=$page&amp;action=new">[Associate publication]</a>|;
 360
 361     }
 362
 363     else { $pub_subtitle= qq|<span class=\"ghosted\">[Associate publication]</span>|;
 364
 365     }
 366
 367
 368     my $pubmed;
 369     my $url_pubmed = qq | http://www.ncbi.nlm.nih.gov/pubmed/|;
 370
 371     my @publications = $population->get_population_publications();
 372     my $abstract_view;
 373     my $abstract_count = 0;
 374
 375
 376
 377     foreach my $pub (@publications) {
 378         my ($title, $abstract, $authors, $journal, $pyear,
 379             $volume, $issue, $pages, $obsolete, $pub_id, $accession
 380            );
 381         $abstract_count++;
 382
 383         my @dbxref_objs = $pub->get_dbxrefs();
 384         my $dbxref_obj = shift(@dbxref_objs);
 385
 386         $obsolete = $population->get_population_dbxref($dbxref_obj)->get_obsolete();
 387
 388         if ($obsolete eq 'f') {
 389             $pub_id = $pub->get_pub_id();
 390             $title = $pub->get_title();
 391             $abstract = $pub->get_abstract();
 392             $pyear = $pub->get_pyear();
 393             $volume = $pub->get_volume();
 394             $journal = $pub->get_series_name();
 395             $pages = $pub->get_pages();
 396             $issue = $pub->get_issue();
 397
 398             $accession = $dbxref_obj->get_accession();
 399             my $pub_info = qq|<a href="/chado/publication.pl?pub_id=$pub_id" >PMID:$accession</a>|;
 400
 401             my @authors;
 402             my $authors;
 403             if ($pub_id) {
 404
 405                 my @pubauthors_ids = $pub->get_pubauthors_ids($pub_id);
 406
 407                 foreach my $pubauthor_id (@pubauthors_ids) {
 408                     my  $pubauthor_obj = CXGN::Chado::Pubauthor->new($self->get_dbh, $pubauthor_id);
 409                     my $last_name  = $pubauthor_obj->get_surname();
 410                     my $first_names = $pubauthor_obj->get_givennames();
 411                     my @first_names = split (/,/, $first_names);
 412                     $first_names = shift (@first_names);
 413                     push @authors, ("$first_names" ."  ". "$last_name");
 414                     $authors = join (", ", @authors);
 415                 }
 416             }
 417
 418
 419
 420
 421             $abstract_view = html_optional_show("abstracts$abstract_count",
 422                                'Show/hide abstract',
 423                                qq|$abstract <b> <i>$authors.</i> $journal. $pyear. $volume($issue). $pages.</b>|,
 424                                                  0, #< do not show by default
 425                                                  'abstract_optional_show', #< don't use the default button-like style
 426                                                 );
 427
 428
 429             $pubmed .= qq| <div><a href="$url_pubmed$accession" target="blank">$pub_info</a> $title $abstract_view</div> |;
 430         }
 431     }
 432
 433     my $is_public = $population->get_privacy_status();
 434     my ($submitter_obj, $submitter_link) = $self->submitter();
 435     my $map_link = $self->genetic_map();
 436     print info_section_html(title   => 'Population Details',
 437                             contents => $population_html,
 438                             );
 439
 440     if ($is_public ||
 441         $login_user_type eq 'curator' ||
 442         $login_user_id ==
 443         $population->get_sp_person_id()
 444        )  {
 445         if ($phenotype_data) {
 446             print info_section_html(title    => 'Phenotype Data and QTLs',
 447                                     contents => $phenotype_data ." ".$data_download
 448                                    );
 449         } else {
 450             print info_section_html(title    => 'Phenotype Data',
 451                                     contents => $accessions_link
 452                                    );
 453         }
 454
 455         unless (!$map_link) {
 456             print info_section_html( title    => 'Genetic Map',
 457                                      contents => $map_link
 458                                    );
 459         }
 460
 461     } else {
 462         my $message = "The QTL data for this population is not public yet.
 463                        If you would like to know more about this data,
 464                        please contact the owner of the data: <b>$submitter_link</b>
 465                        or email to SGN:
 466                        <a href=mailto:sgn-feedback\@sgn.cornell.edu>
 467                        sgn-feedback\@sgn.cornell.edu</a>.\n";
 468
 469         print info_section_html(title   => 'Phenotype Data and QTLs',
 470                                 contents =>$message,
 471                                );
 472
 473     }
 474     print info_section_html(title   => 'Literature Annotation',
 475                             #subtitle => $pub_subtitle,
 476                             contents => $pubmed,
 477                             );
 478
 479     if ($population_name) {
 480         # change sgn_people.forum_topic.page_type and the CHECK constraint!!
 481         my $page_comment_obj = CXGN::People::PageComment->new($self->get_dbh(), "population", $population_id, $self->get_page()->{request}->uri()."?".$self->get_page()->{request}->args());
 482         print $page_comment_obj->get_html();
 483     }
 484
 485     $self->get_page()->footer();
 486
 487
 488     exit();
 489 }
 490
 491
 492
 493
 494
 495
 496 # override store to check if a locus with the submitted symbol/name already exists in the database
 497
 498 sub store {
 499    my $self = shift;
 500    my $population = $self->get_object();
 501    my $population_id = $self->get_object_id();
 502    my %args = $self->get_args();
 503
 504    $self->SUPER::store(0);
 505
 506  exit();
 507 }
 508
 509
 510 sub submitter {
 511     my $self = shift;
 512     my $population = $self->get_object();
 513     my $sp_person_id= $population->get_sp_person_id();
 514     my $submitter = CXGN::People::Person->new($self->get_dbh(), $population->get_sp_person_id());
 515     my $submitter_name = $submitter->get_first_name()." ".$submitter->get_last_name();
 516     my $submitter_link = qq |<a href="/solpeople/personal-info.pl?sp_person_id=$sp_person_id">$submitter_name</a> |;
 517
 518     return $submitter, $submitter_link;
 519
 520 }
 521
 522 sub genetic_map {
 523     my $self     = shift;
 524     my $mapv_id  = $self->get_object()->mapversion_id();
 525
 526     if ($mapv_id) {
 527         my $map      = CXGN::Map->new( $self->get_dbh(), { map_version_id => $mapv_id } );
 528         my $map_name = $map->get_long_name();
 529         my $map_sh_name = $map->get_short_name();
 530         my $genetic_map =
 531             qq | <a href=/cview/map.pl?map_version_id=$mapv_id>$map_name ($map_sh_name)</a>|;
 532
 533         return $genetic_map;
 534     }
 535     else {
 536         return;
 537     }
 538
 539 }
 540
 541
 542