cgi-bin/phenome/individual.pl

   1 use strict;
   2
   3 my $individual_detail_page = CXGN::Phenome::IndividualDetailPage->new();
   4
   5 package CXGN::Phenome::IndividualDetailPage;
   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 use SGN::Image;
  18 use CXGN::Phenome::Individual;
  19 use CXGN::Phenome::Population;
  20 use CXGN::Chado::Publication;
  21 use CXGN::People::PageComment;
  22 use CXGN::People::Person;
  23 use CXGN::Cview::Map_overviews;
  24 use CXGN::Contact;
  25 use CXGN::Feed;
  26 use CXGN::Tools::Organism;
  27 use JSAN::ServerSide;
  28 use HTML::Entities;
  29
  30 use base qw / CXGN::Page::Form::SimpleFormPage /;
  31
  32 sub new {
  33     my $class = shift;
  34     my $self = $class->SUPER::new(@_);
  35     $self->set_script_name("individual.pl");
  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 $individual_id= $args{individual_id};
  49     my $individual_name= $args{individual_name};
  50     if ($individual_name && !$individual_id ) {
  51         my $individual_by_name = (CXGN::Phenome::Individual->new_with_name($self->get_dbh(), $individual_name))[0];
  52         if ($individual_by_name) { $individual_id = $individual_by_name->get_individual_id(); }
  53     }
  54
  55     unless ( ( $individual_id =~ m /^\d+$/  ) || ($args{action} eq 'new' && !$individual_id) )
  56     {
  57         $c->throw(is_error=>0,
  58                   message=>"No accession exists for identifier $individual_id",
  59             );
  60     }
  61     my $individual=CXGN::Phenome::Individual->new($self->get_dbh(),$individual_id ) ;
  62     $self->set_object_id($individual_id);
  63     $self->set_object($individual);
  64     $self->set_primary_key("individual_id");
  65
  66
  67     if ( $individual->get_obsolete() eq 't' && $self->get_user()->get_user_type() ne 'curator' )
  68     {
  69         $c->throw(is_error=>0,
  70                   title => 'Obsolete accession',
  71                   message=>"Accession $individual_id is obsolete!",
  72                   developer_message => 'only curators can see obsolete accessions',
  73                   notify => 0,   #< does not send an error email
  74             );
  75     }
  76     my $action= $args{action};
  77     if ( !$individual->get_individual_id() && $action ne 'new'  ) {
  78         $c->throw(is_error=>0, message=>'No accession exists for this identifier',);
  79     }
  80
  81     $self->set_owners($self->get_object()->get_owners());
  82 }
  83
  84
  85 sub delete {
  86     my $self = shift;
  87     $self->check_modify_privileges();
  88     my $individual = $self->get_object();
  89     my %args = $self->get_args();
  90
  91     eval {
  92         $individual->delete();
  93     };
  94     if ($@) {
  95         $self->get_page()->message_page("An error occurred during deletion of the accession.");
  96     }
  97
  98     $self->get_page()->header();
  99
 100     print qq {
 101         The accession has been successfully deleted.  };
 102     $self->get_page()->footer();
 103     exit();
 104 }
 105
 106
 107 sub generate_form {
 108     my $self = shift;
 109
 110     $self->init_form();
 111
 112     my %args = $self->get_args();
 113
 114     my $individual = $self->get_object();
 115     my $type_id = $args{type_id};
 116     my $type=$args{type};
 117
 118     #my $individual_id = $self->get_object_id();
 119     my $sp_person_id= $individual->get_sp_person_id();
 120     my $submitter = CXGN::People::Person->new($self->get_dbh(), $individual->get_sp_person_id());
 121     my $submitter_name = $submitter->get_first_name()." ".$submitter->get_last_name();
 122     my $submitter_link = qq |<a href="/solpeople/personal-info.pl?sp_person_id=$sp_person_id">$submitter_name </a> |;
 123     my $pop_name = $individual->get_population_name();
 124     my $pop_id = $individual->get_population_id();
 125     my $pop_link = qq |<a href="/phenome/population.pl?population_id=$pop_id">$pop_name </a> |;
 126     my $population_names_ref = CXGN::Phenome::Population::get_all_populations($self->get_dbh());
 127
 128     my @p_names= map {$_->[1]} (@$population_names_ref);
 129     my @p_ids=   map {$_->[0]} (@$population_names_ref);
 130     my ($organism_names_ref, $organism_ids_ref) = CXGN::Tools::Organism::get_all_organisms($self->get_dbh());
 131
 132     my $form = undef;
 133     if ($self->get_action()=~/new|edit|store/ ) {
 134         $form = CXGN::Page::Form::Editable->new();
 135     }
 136     else {
 137         $form = CXGN::Page::Form::Static->new();
 138     }
 139
 140     $form->add_field(
 141                       display_name=>"Accession",
 142                       field_name=>"name",
 143                       length=>15,
 144                       object=>$individual,
 145                       getter=>"get_name",
 146                       setter=>"set_name",
 147                       validate => 'string',
 148                       );
 149     $form->add_textarea(
 150                           display_name=>"Description",
 151                           field_name=>"description",
 152                           object=>$individual,
 153                           getter=>"get_description", setter=>"set_description",
 154                           columns => 40,
 155                           rows =>4,
 156                           );
 157
 158
 159
 160     if ($self->get_action=~ /new|store/) {
 161         $form->add_select(
 162                           display_name => "Population",
 163                           field_name  => "population_id",
 164                           contents =>$individual->get_population_id(),
 165                           length=> 20,
 166                           object => $individual,
 167                           getter => "get_population_id",
 168                           setter => "set_population_id",
 169                           select_list_ref => \@p_names,
 170                           select_id_list_ref=>\@p_ids,
 171                           );
 172         $form->add_select(
 173                           display_name => "Organism",
 174                           field_name  => "common_name_id",
 175                           contents =>$individual->get_common_name_id(),
 176                           length=> 20,
 177                           object => $individual,
 178                           getter => "get_common_name_id",
 179                           setter => "set_common_name_id",
 180                           select_list_ref => $organism_names_ref,
 181                           select_id_list_ref=> $organism_ids_ref,
 182                           );
 183     } else {
 184         $form->add_label( display_name=>"Population",
 185                           field_name=>"population_name",
 186                           contents=>$pop_link,
 187                           );
 188         $form->add_label( display_name=>"Organism",
 189                           field_name=>"common_name",
 190                           contents=>$individual->get_common_name(),
 191                           );
 192     }
 193
 194     $form->add_hidden( field_name=>"individual_id", contents=>$args{individual_id});
 195     $form->add_hidden( field_name=>"action", contents=>"store"  );
 196     $form->add_hidden (
 197                        field_name => "sp_person_id",
 198                        contents   =>$self->get_user()->get_sp_person_id(),
 199                        object     => $individual,
 200                        setter     =>"set_sp_person_id",
 201                        );
 202
 203     $form->add_hidden (
 204                        field_name => "updated_by",
 205                        contents   =>$self->get_user()->get_sp_person_id(),
 206                        object     => $individual,
 207                        setter     =>"set_updated_by",
 208                        );
 209
 210     $form->add_hidden( field_name=>"type", contents=>$args{type} );
 211     $form->add_hidden( field_name=>"type_id", contents=>$args{type_id} );
 212
 213     #$form->add_hidden( field_name=>"locus_id", contents=>$locus_id);
 214
 215     $self->set_form($form);
 216
 217     if ($self->get_action=~ /view|edit/) {
 218         $self->get_form->from_database();
 219
 220         $form->add_hidden (
 221                            field_name => "population_id",
 222                            contents   =>$individual->get_population_id(),
 223                            );
 224
 225         $form->add_label( display_name=>"Uploaded by",
 226                           field_name=>"submitter",
 227                           contents=>$submitter_link,
 228                           );
 229
 230     }elsif ($self->get_action=~ /store/) {
 231         $self->get_form->from_request($self->get_args());
 232         #if ($type && $type_id) {
 233         if ($type eq "locus") { $individual->associate_locus(); }
 234         elsif ($type eq "allele") { $individual->associate_allele($type_id, $self->get_user()->get_sp_person_id() ); }
 235         my $subject="[New accession details stored] individual $args{individual_id}";
 236         my $username= $self->get_user()->get_first_name()." ".$self->get_user()->get_last_name();
 237         my $sp_person_id=$self->get_user()->get_sp_person_id();
 238         my $usermail=$self->get_user()->get_private_email();
 239         my $fdbk_body="$username has submitted data for individual $args{individual_id}\nsp_person_id = $sp_person_id, $usermail";
 240         CXGN::Contact::send_email($subject,$fdbk_body, 'sgn-db-curation@sgn.cornell.edu');
 241         CXGN::Feed::update_feed($subject,$fdbk_body);
 242         #}
 243     }
 244 }
 245
 246 sub display_page {
 247     my $self = shift;
 248     my %args = $self->get_args();
 249
 250     my $individual = $self->get_object();
 251     my $individual_id = $self->get_object_id();
 252     my $individual_name = $individual->get_name();
 253
 254     #insert the necessary javascript for the ajax forms in this page
 255     #$self->add_javascript();
 256     $self->get_page->jsan_use("CXGN.Phenome.Individual");
 257     $self->get_page->jsan_use("CXGN.Phenome.Tools");
 258
 259     $self->get_page->jsan_use("MochiKit.DOM");
 260     $self->get_page->jsan_use("Prototype");
 261     $self->get_page->jsan_use("jQuery");
 262     $self->get_page->jsan_use("thickbox");
 263
 264      my $action = $args{action};
 265     if (!$individual_id && $action ne 'new' && $action ne 'store') { $self->get_page->message_page("No accession exists for this identifier"); }
 266
 267     #used to show certain elements to only the proper users
 268     my $login_user= $self->get_user();
 269     my $login_user_id= $login_user->get_sp_person_id();
 270     my $login_user_type= $login_user->get_user_type();
 271
 272     my $tag_link = qq { <a href="tag.pl?individual_id=$individual_id&amp;action=new">Add tag</a> };
 273
 274     $self->get_page()->header("SGN accession name: $individual_name");
 275
 276     print page_title_html("SGN accession: $individual_name \n");
 277
 278     my $page="../phenome/individual.pl?individual_id=$individual_id";
 279     $args{calling_page} = $page;
 280
 281     my $individual_html = $self->get_edit_links()."<br />";
 282
 283     #print all editable form  fields
 284     $individual_html .= $self->get_form()->as_table_string();
 285
 286      ##############history:
 287
 288     my $object_owner = $individual->get_sp_person_id();
 289     if ($login_user_type eq 'curator' || $login_user_id == $object_owner) {
 290
 291         my $history_data= $self->print_individual_history();
 292
 293         $individual_html .= $history_data;
 294     }
 295     ####### print associated loci
 296     $individual_html .=  qq { <br /><br /><b>Associated loci:</b>  };
 297     my @loci = $individual->get_loci();
 298     foreach my $locus (@loci) {
 299         unless ($locus->get_obsolete() eq 't') {
 300             my $locus_id = $locus->get_locus_id();
 301             my $locus_name = $locus->get_locus_name();
 302             $individual_html .=qq{&nbsp<a href ="locus_display.pl?locus_id=$locus_id">$locus_name </a>&nbsp};
 303         }
 304     }
 305     #######associate locus
 306     if ($login_user_type eq 'curator' || $login_user_type eq 'submitter' || $login_user_type eq 'sequencer') {
 307         if ($individual_name) {  $individual_html .= $self->associate_loci();  }
 308     } else { $individual_html .= qq |<span class = "ghosted"> [Associate locus]</span><br /> |; }
 309
 310
 311     ####### dbxref data: ontology annotations, publications...:
 312     my ($xref_source, $pubs, $pub_count, $genbank, $gb_count, $onto_ref) = $self->get_dbxref_info();
 313
 314     $individual_html .= $xref_source;
 315
 316      print info_section_html(title   => 'Accession details',
 317                             contents => $individual_html,
 318                             );
 319     ##############images:
 320
 321     my $image_html;
 322     #$image_html .=qq|<table><tr valign="top">|;
 323     my @images = $individual->get_image_ids();  #array of associated image objects
 324     my $image_count = 0;
 325
 326     $image_html .=qq|<table><tr valign="top">|;
 327
 328     foreach my $image_id (@images) {
 329         $image_count ++;
 330         if ($image_count == 8) {
 331             $image_html .= qq|</tr><tr valign="top">|;
 332             $image_count=1;
 333         }
 334         my $image=SGN::Image->new($individual->get_dbh(), $image_id);
 335         my $small_image=$image->get_image_url("thumbnail");
 336         my $medium_image=$image->get_image_url("medium");
 337         my $image_page= "/image/index.pl?image_id=$image_id";
 338         $image_html .=qq|<td><a href="$medium_image" title="<a href=$image_page>Go to image page </a>" class="thickbox" rel="gallery-images"><img src="$small_image" alt="" /></a></td> |;
 339     }
 340     $image_html .= "</tr></table>";
 341     #link for adding new images
 342     if ($individual_name)
 343     { $image_html .=
 344           qq|<br /><a href="../image/add_image.pl?type_id=$individual_id&amp;action=new&amp;type=individual&amp;refering_page=$page">[Add new image]</a>|;
 345     }
 346
 347
 348     print info_section_html(title   => 'Images',
 349                             contents => $image_html,
 350                             );
 351
 352
 353 ############################### PHENOTYPE DATA
 354
 355
 356     my @phenotypes= $individual->get_phenotypes();
 357     my $population_obj = $individual->get_population();
 358     my @phenotype;
 359     my ($data_view, $term_obj, $term_name, $term_id, $min, $max, $ave, $value);
 360
 361     foreach my $p (@phenotypes)
 362     {
 363
 364         if (!$population_obj->get_web_uploaded())
 365         {
 366             $term_obj  = CXGN::Chado::Cvterm->new( $self->get_dbh(), $p->get_observable_id());
 367             $term_name = $term_obj->get_cvterm_name();
 368             $term_id   = $term_obj->get_cvterm_id();
 369             ($min, $max, $ave) = $population_obj->get_pop_data_summary($term_id);
 370             $value = $p->get_value();
 371             if (!defined($value)) {$value= 'N/A';}
 372             elsif ($value == 0) {$value = '0.0';}
 373
 374
 375         } else
 376         {
 377             $term_obj  = CXGN::Phenome::UserTrait->new($self->get_dbh(), $p->get_observable_id());
 378             $term_name = $term_obj->get_name();
 379             $term_id   = $term_obj->get_user_trait_id();
 380             ($min, $max, $ave) = $population_obj->get_pop_data_summary($term_id);
 381             $value = $p->get_value();
 382         }
 383
 384         $term_obj  = CXGN::Chado::Cvterm::get_cvterm_by_name( $self->get_dbh(), $term_name);
 385         my $cvterm_id = $term_obj->get_cvterm_id();
 386
 387         if ($cvterm_id)
 388         {
 389             $term_id = $term_obj->get_cvterm_id();
 390             if ($term_obj->get_definition() )
 391             {
 392                 push  @phenotype,  [map {$_}
 393                                     ((tooltipped_text(qq|<a href="/chado/cvterm.pl?cvterm_id=$term_id">$term_name</a>|,
 394                                                       $term_obj->get_definition() )), $value, $min, $max, $ave) ];
 395             }else
 396             {
 397                 push  @phenotype,  [map {$_} qq|<a href="/chado/cvterm.pl?cvterm_id=$term_id">$term_name</a>|,
 398                                     $value, $min, $max, $ave ];
 399             }
 400         }
 401         else
 402         {
 403             if ($term_obj->get_definition() )
 404             {
 405                 push  @phenotype,  [map {$_}
 406                                     ((tooltipped_text(qq|<a href="/phenome/trait.pl?trait_id=$term_id">$term_name</a>|,
 407                                                       $term_obj->get_definition() )), $value, $min, $max, $ave) ];
 408             }else {
 409                 push  @phenotype,  [map {$_} qq|<a href="/phenome/trait.pl?trait_id=$term_id">$term_name</a>|,
 410                                     $value, $min, $max, $ave ];
 411             }
 412         }
 413     }
 414
 415     if (@phenotype) {
 416         my $phenotype_data .= columnar_table_html(
 417                                                 headings  =>
 418                                                     [
 419                                                     'Trait',
 420                                                     'Value',
 421                                                     'Pop min',
 422                                                     'Pop max',
 423                                                     'Pop mean',
 424                                                     ],
 425                                                    data     =>\@phenotype,
 426                                                   __alt_freq   =>2,
 427                                                   __alt_width  =>1,
 428                                                   __alt_offset =>3,
 429                                                   __align =>'l',
 430                                                   );
 431
 432         $data_view = html_optional_show("phenotype",
 433                                         'View/hide phenotype data summary',
 434                                         qq|$phenotype_data|,
 435                                         1, #<  show data by default
 436             );
 437     }
 438
 439     print info_section_html(title   => 'Phenotype data',
 440                             contents => $data_view,
 441                             );
 442
 443  ######## map:
 444
 445     my $overview = CXGN::Cview::Map_overviews::Individual->new($individual_id);
 446     my $map_html;
 447     if ($overview) {
 448         $overview->render_map();
 449         #my ($url, $path) = $overview->get_file_png();
 450
 451         $map_html .= $overview->get_image_html();
 452     }
 453     print info_section_html(title   => 'Mapping data',
 454                             contents => $map_html,
 455                             );
 456
 457     ######## alleles:
 458
 459     my @alleles = $individual->get_alleles(); #array of associated allele objects
 460     my @allele_data;
 461     my $allele_data;
 462     foreach my $allele(@alleles) {
 463         my $allele_id= $allele->get_allele_id();
 464         my $locus_id = $allele->get_locus_id();
 465         my $locus= CXGN::Phenome::Locus->new($self->get_dbh(), $locus_id);
 466         my $locus_name= $locus->get_locus_name();
 467         my $phenotype = $allele->get_allele_phenotype();
 468
 469         push @allele_data, [map {$_} ( qq|<a href= "locus_display.pl?locus_id=$locus_id">$locus_name</a>|,
 470                                        $allele->get_allele_symbol(), qq|<div align="left"><a href= "allele.pl?allele_id=$allele_id">$phenotype</a></div>|,)
 471                             ];
 472     }
 473
 474     if (@allele_data) {
 475         $allele_data .=columnar_table_html(headings => ['Locus name', 'Allele symbol', 'Phenotype',],
 476                                            data     =>\@allele_data,
 477                                            );
 478     }
 479     print info_section_html(title =>'Known alleles',
 480                             contents => $allele_data,
 481                             );
 482
 483 ####### Germplasms:
 484
 485     my $germplasm_data="";
 486     my @germplasms= $individual->get_germplasms(); #array of associated germplasm objects
 487
 488     print info_section_html(title =>'Available germplasms',
 489                             contents => $germplasm_data,
 490                             );
 491
 492     ##########literature ########################################
 493     my ($pub_links, $pub_subtitle);
 494     if ($pubs) {
 495         $pub_links = info_table_html( "  "    =>$pubs,
 496                                       __border => 0,
 497                                       );
 498     }
 499
 500     if ($individual_name && ($login_user_type eq 'curator' || $login_user_type eq 'submitter' || $login_user_type eq 'sequencer')) {
 501         $pub_subtitle .= qq|<a href="/chado/add_publication.pl?type=individual&amp;type_id=$individual_id&amp;refering_page=$page&amp;action=new"> [Associate publication] </a>|;
 502     }else { $pub_subtitle= qq|<span class=\"ghosted\">[Associate publication]</span>|;}
 503
 504
 505     print info_section_html(title   => "Literature annotation ($pub_count)",
 506                             subtitle=> $pub_subtitle,
 507                             contents =>$pub_links,
 508                             collapsible=>1,
 509                             collapsed=>1,
 510                             );
 511
 512
 513  ######################################## Ontology details ##############
 514
 515     my ($ontology_links, $ontology_evidence, $ontology_info);
 516     my $onto_hash;
 517     #my ($po_str, $po_gro, $sp) ;
 518     #my ( @po_str_evidence, @po_gro_evidence, @sp);
 519
 520     my @obs_annot;
 521     my $ont_count=0 ;
 522     my %ont_hash=(); #keys= cvterms, values= hash of arrays (keys= ontology details, values= list of evidences)
 523     foreach (@$onto_ref ) {   # ([dbxref_object, ind_dbxref_obsolete])
 524         my $cv_name= $_->[0]->get_cv_name();
 525         my $cvterm_id= $_->[0]->get_cvterm_id();
 526         my $cvterm_name= $_->[0]->get_cvterm_name();
 527         my $db_name= $_->[0]->get_db_name();
 528         my $accession = $_->[0]->get_accession();
 529         my $db_accession = $accession;
 530         $db_accession= $cvterm_id if $db_name eq 'SP';
 531         my $url=  $_->[0]->get_urlprefix() .  $_->[0]->get_url();
 532         my $cvterm_link= qq |<a href="/chado/cvterm.pl?cvterm_id=$cvterm_id" target="blank">$cvterm_name</a>|;
 533         my $ind_dbxref= $individual->get_individual_dbxref($_->[0]);
 534         my @AoH= $ind_dbxref->evidence_details();
 535
 536         for my $href (@AoH) {
 537             my $relationship= $href->{relationship};
 538
 539             if ($href->{obsolete} eq 't') {
 540                 push @obs_annot, $href->{relationship}." ".$cvterm_link." (".$href->{ev_code}.")"
 541                     . $self->unobsolete_ev($href->{dbxref_ev_object});
 542             }else {
 543                 my $ontology_details= $href->{relationship}.qq| $cvterm_link ($db_name:<a href="$url$db_accession" target="blank"> $accession</a>)<br />|;
 544                 # add an empty row if there is more than 1 evidence code
 545                 my $ev_string;
 546                 $ev_string .= "<br /><hr>" if $ont_hash{$cv_name}{$ontology_details};
 547                 $ev_string .= $href->{ev_code}."<br />". $href->{ev_desc}."<br /><a href=\"". $href->{ev_with_url}. "\">" . $href->{ev_with_acc} . "</a><br /><a href=\"" . $href->{reference_url} ."\">" . $href->{reference_acc} . "</a><br />".$href->{submitter}. $self->get_ev_obs_link($href->{dbxref_ev_object}) ;
 548                 $ont_hash{$cv_name}{$ontology_details} .= $ev_string ;
 549             }
 550         }
 551     }
 552
 553     #now we should have an %ont_hash with all the details we need for printing ...
 554     #hash keys are the cv names ..
 555     for my $cv_name (sort keys %ont_hash) {
 556         my @evidence;
 557         #create a string of ontology details from the end level hash keys, which are the values of each cv_name
 558         my $cv_ont_details;
 559         #and for each ontology annotation create an array ref of evidences
 560         for my $ont_detail (sort keys  %{ $ont_hash{$cv_name} } ) {
 561             $ont_count++;
 562             $cv_ont_details .= $ont_detail ;
 563             push @evidence, [$ont_detail, $ont_hash{$cv_name}{$ont_detail}];
 564         }
 565         $ontology_links .= info_table_html($cv_name=> $cv_ont_details,
 566                                            __border=>0,
 567             );
 568         my $ev_table= columnar_table_html(data=>\@evidence,__align=>'lll',__alt_freq=>2,__alt_offset => 1);
 569         $ontology_evidence .= info_table_html($cv_name=>$ev_table, __border=>0,__tableattrs=>'width="100%"',);
 570     }
 571
 572     #display ontology annotation form
 573     my $ontology_add_link;
 574     my $ontology_subtitle;
 575     if (($login_user_type eq 'curator' || $login_user_type eq 'submitter' || $login_user_type eq 'sequencer') ) {
 576         if ($individual_name) {
 577             if (@obs_annot) { $ontology_links .=print_obsoleted(@obs_annot) } ;
 578             $ontology_subtitle .= qq|<a href="javascript:Tools.toggleContent('associateOntForm', 'individual_ontology')">[Add ontology annotation]</a> |;
 579             $ontology_add_link= $self->associate_ontology_term();
 580         }
 581     }else { $ontology_subtitle =qq |<span class = "ghosted"> [Add ontology annotations]</span> |; }
 582
 583     $ontology_info .=$ontology_add_link;#the javascript form for adding new annotations
 584         if ($ontology_evidence) {
 585
 586             $ontology_info .=  html_alternate_show('ontology_annotation',
 587                                                   'Annotation info',
 588                                                   $ontology_links,
 589                                                   $ontology_evidence,
 590                                                   );
 591         }else { $ontology_info .= $ontology_links; }
 592     print info_section_html(title =>"Ontology annotations ($ont_count)",
 593                             subtitle=>$ontology_subtitle,
 594                             contents => $ontology_info,
 595                             id      =>"individual_ontology",
 596                             collapsible=>1,
 597         );
 598
 599     ###########Page comments############
 600     if ($individual_name) {
 601         # change sgn_people.forum_topic.page_type and the CHECK constraint!!
 602         my $page_comment_obj = CXGN::People::PageComment->new($self->get_dbh(), "individual", $individual_id);
 603         print $page_comment_obj->get_html();
 604     }
 605     ######################################3
 606
 607     $self->get_page()->footer();
 608     exit();
 609 }
 610
 611 sub print_individual_history {
 612     my $self=shift;
 613     my $individual=$self->get_object();
 614
 615     my @history;
 616     my $history_data;
 617     my $print_history;
 618     my @history_objs = $individual->show_history(); #array of individual_history objects
 619
 620     foreach my $h (@history_objs) {
 621
 622         my $created_date= $h->get_create_date();
 623         $created_date = substr $created_date, 0, 10;
 624
 625         my $history_id = $h->{individual_history_id};
 626         my $updated_by_id= $h->{updated_by};
 627         my $updated=CXGN::People::Person->new($self->get_dbh(), $updated_by_id);
 628         my $u_first_name = $updated->get_first_name();
 629         my $u_last_name = $updated->get_last_name();
 630         my $up_person_link =qq |<a href="/solpeople/personal-info.pl?sp_person_id=$updated_by_id">$u_first_name $u_last_name</a> ($created_date)|;
 631
 632         push @history, [map {$_} ($h->get_name,$h->get_description,$h->get_population()->get_name(),
 633                                   $up_person_link,)
 634                         ];
 635     }
 636
 637     if (@history) {
 638         $history_data .= columnar_table_html(headings => ['Name',
 639                                                           'Description',
 640                                                           'Population',
 641                                                           'Updated by',
 642                                              ],
 643                                              data     =>\@history,
 644                                              __alt_freq   =>2,
 645                                              __alt_width  =>1,
 646                                              __alt_offset =>3,
 647             );
 648         $print_history=
 649             html_optional_show('accession_history',
 650                                'Show accession history',
 651                                qq|<div class="minorbox">$history_data</div> |,
 652             );
 653     }
 654
 655     return $print_history;
 656 }#print_individual_history
 657
 658
 659 # override store to check if a locus with the submitted symbol/name already exists in the database
 660
 661 sub store {
 662    my $self = shift;
 663    my $individual = $self->get_object();
 664    my $individual_id = $self->get_object_id();
 665    my %args = $self->get_args();
 666
 667
 668    my $message = $individual->exists_in_database( $args{name} );
 669
 670    if ($message ) {#&& $name_id!= $locus_id && $name_obsolete==0 ) {
 671        $self->get_page()->message_page($message);
 672    } else {
 673        $self->SUPER::store(0);
 674    }
 675 }
 676
 677
 678 sub get_ev_obs_link {
 679     my $self =shift;
 680     my $ind=$self->get_object();
 681     my $ev_dbxref=shift;
 682     my $delete_link = "";
 683     my $user_type= $self->get_user->get_user_type();
 684     my $logged_user= $self->get_user()->get_sp_person_id();
 685     my $ev_dbxref_id= $ev_dbxref->get_object_dbxref_evidence_id();
 686     #check obsolete permissions. Granted for
 687     #curators, the individual owner(s) and the submitter of the annotation
 688     #(in this case we go by the evidence code, since annotations can have multiple evidences)
 689     if (($ind->get_sp_person_id == $logged_user) || ($ev_dbxref->get_sp_person_id() == $logged_user) || ($user_type eq 'curator' ) ) {
 690         $delete_link=qq|
 691             <a href="javascript:Tools.obsoleteAnnotEv('individual', '$ev_dbxref_id')">[delete]</a><br>
 692
 693             <div id='obsoleteIndividualOntologyForm' style="display: none">
 694             <div id='ev_dbxref_id_hidden'>
 695                        <input type="hidden"
 696                        value=$ev_dbxref_id
 697                        id="$ev_dbxref_id">
 698                        </div>
 699             </div>
 700             |;
 701     }
 702 }
 703
 704 sub unobsolete_ev {
 705     my $self =shift;
 706     my $ind=$self->get_object();
 707     my $ev_dbxref= shift;
 708     my $ev_dbxref_id= $ev_dbxref->get_object_dbxref_evidence_id();
 709     my $unobsolete_link = "";
 710
 711     if (($self->get_user()->get_user_type() eq 'submitter') || ($self->get_user()->get_user_type() eq 'curator') || ($self->get_user()->get_user_type() eq 'sequencer')) {
 712         $unobsolete_link=qq|
 713             <a href="javascript:Tools.unobsoleteAnnotEv('individual','$ev_dbxref_id')">[unobsolete]</a>
 714
 715             <div id='unobsoleteAnnotationForm' style="display: none">
 716             <div id='ev_dbxref_id_hidden'>
 717             <input type="hidden"
 718             value=$ev_dbxref_id
 719             id="$ev_dbxref_id">
 720             </div>
 721             </div>
 722             |;
 723     }
 724     return $unobsolete_link;
 725 }
 726
 727
 728 ########################
 729
 730 sub print_obsoleted {
 731     my @ontology_terms=@_;
 732     my $obsoleted;
 733     foreach my $term (@ontology_terms) {
 734         $obsoleted .=  qq |$term  <br />\n |;
 735     }
 736     my $print_obsoleted=
 737         html_optional_show('obsoleted_terms',
 738                            'Show obsolete',
 739                            qq|<div class="minorbox">$obsoleted</div> |,
 740                            );
 741     return $print_obsoleted;
 742
 743 }
 744
 745
 746 sub get_dbxref_info {
 747     my $self=shift;
 748     my $ind=$self->get_object();
 749     my $ind_name=$ind->get_name();
 750     my %dbs = $ind->get_dbxref_lists(); #hash of arrays. keys=dbname values= dbxref objects
 751     my ($xref_source, $pubs, $genbank, $onto_ref, $ont_ev,$obs_annot);
 752     ##tgrc
 753     foreach (@{$dbs{'TGRC_accession'}} ) {
 754         if ($_->[1] eq '0') {
 755             my $url= $_->[0]->get_urlprefix() . $_->[0]->get_url();
 756             my $accession= $_->[0]->get_accession();
 757             $xref_source .= qq|$ind_name is a <a href="$url$accession" target="blank">TGRC accession</a><br />|;
 758         }
 759     }
 760     foreach (@{$dbs{'EUSOL:accession'}} ) {
 761         if ($_->[1] eq '0') {
 762             my $url= $_->[0]->get_urlprefix() . $_->[0]->get_url();
 763             my $accession= $_->[0]->get_accession();
 764             $xref_source .= qq|<br />Available at  <br /><a href="$url$accession" target="blank"><img src= "/documents/img/eusol_logo_small.jpg" border="0" /></a><br />|;
 765         }
 766     }
 767     my $abs_count=0;
 768     foreach (@{$dbs{'PMID'}} ) {
 769         $pubs .= $self->get_pub_info($_->[0],$abs_count++) if $_->[1] eq '0'; }
 770     foreach (@ {$dbs{'SGN_ref'}} ) { $pubs .= $self->get_pub_info($_->[0],$abs_count++) if $_->[1] eq '0'; }
 771     my @pop_dbxrefs=$ind->get_population()->get_all_population_dbxrefs();
 772     foreach (@pop_dbxrefs) {
 773         my $db_name = $_->get_db_name();
 774         if ($db_name eq 'PMID' || $db_name eq  'SGN_ref' ) {
 775             $pubs .= $self->get_pub_info($_, $abs_count++);
 776         }
 777     }
 778     my $gb_count=0;
 779     foreach (@{$dbs{'DB:GenBank_GI'}} ) {
 780         if ($_->[1] eq '0') {
 781             $gb_count++;
 782             my $url= $_->[0]->get_urlprefix() . $_->[0]->get_url();
 783             my $gb_accession=$self->CXGN::Chado::Feature::get_feature_name_by_gi($_->[0]->get_accession());
 784             my $description=$_->[0]->get_description();
 785             $genbank .=qq|<a href="$url$gb_accession" target="blank">$gb_accession</a> $description<br />|;
 786         }
 787     }
 788     my @ont_annot;
 789     foreach ( @{$dbs{'GO'}}) { push @ont_annot, $_; }
 790     foreach ( @{$dbs{'PO'}}) { push @ont_annot, $_; }
 791     foreach ( @{$dbs{'SP'}}) { push @ont_annot, $_; }
 792
 793     return ($xref_source, $pubs, $abs_count, $genbank, $gb_count, \@ont_annot);
 794 }
 795
 796 sub abstract_view {
 797     my $self=shift;
 798     my $pub=shift;
 799     my $abs_count=shift;
 800     my $abstract=encode_entities($pub->get_abstract());
 801     my $authors=encode_entities($pub->get_authors_as_string() ) ;#self->author_info($pub->get_pub_id());
 802     my $journal=$pub->get_series_name() ;
 803     my $pyear=$pub->get_pyear();
 804     my $volume=$pub->get_volume() ;
 805     my $issue=$pub->get_issue();
 806     my $pages=$pub->get_pages();
 807     my $abstract_view = html_optional_show("abstracts$abs_count",
 808                                            'Show/hide abstract',
 809                                            qq|$abstract <b> <i>$authors.</i> $journal. $pyear. $volume($issue). $pages. </b>|,
 810                                            0, #< do not show by default
 811                                            'abstract_optional_show', #< don't use the default button-like style
 812                                            );
 813     return $abstract_view;
 814 }#
 815
 816 sub get_pub_info {
 817     my $self=shift;
 818     my ($dbxref,  $count)=@_;
 819     my $db=$dbxref->get_db_name();
 820     my $pub_info;
 821     my $accession= $dbxref->get_accession();
 822     my $pub_title=$dbxref->get_publication()->get_title();
 823     my $pub_id= $dbxref->get_publication()->get_pub_id();
 824     my $abstract_view=$self->abstract_view($dbxref->get_publication(), $count);
 825     $pub_info = qq|<div><a href="/chado/publication.pl?pub_id=$pub_id" >$db:$accession</a> $pub_title $abstract_view </div> |;
 826     return $pub_info;
 827 }#
 828
 829
 830 #################################
 831 sub associate_loci {
 832     my $self=shift;
 833     my $individual_id=$self->get_object_id();
 834     my $sp_person_id= $self->get_user->get_sp_person_id();
 835     my $user_type = $self->get_user->get_user_type();
 836    # my $locus_tip= tooltipped_text('Locus name or symbol', 'To filter your locus search by the organism of interest, enter a locus name or symbol followed by comma and the organism name (eg. flower, tomato).');
 837     my $associate_html = qq^
 838 <br><a href=javascript:Individual.toggleAssociateFormDisplay()>[associate new locus]</a>
 839 <div id="associationForm" style="display: none">
 840
 841        <input type="text"
 842                style="width: 50%"
 843                id="locus_name"
 844                onkeyup="Tools.getLoci(this.value, '$individual_id');">
 845        <select id = "organism_select" onchange="Tools.getLoci( MochiKit.DOM.getElement('locus_name').value, '$individual_id')">
 846                   <option value="Tomato">tomato</option>
 847                   <option value="Potato">potato</option>
 848                   <option value="Pepper">pepper</option>
 849                   <option value="Eggplant">eggplant</option>
 850                   <option value="Coffee">coffee</option>
 851          </select>
 852                <select id="locus_select"
 853                 style="width: 100%"
 854                 size=10
 855                 onchange="Individual.getAlleles(this.value, '$individual_id');MochiKit.DOM.getElement('associate_locus_button').disabled=false;">
 856         </select>
 857         <span id ="alleleSelect" style="display: none">
 858             <b>Would you Like to specify an allele?</b>
 859             <select id="allele_select"
 860                     style="width: 100%">
 861             </select>
 862         </span>
 863         <input type="button"
 864                id="associate_locus_button"
 865                value="associate locus"
 866                disabled="true"
 867                onclick="Individual.associateAllele('$sp_person_id', '$individual_id');this.disabled=true;">
 868     </div><br><br>^;
 869
 870     return $associate_html;
 871 }
 872
 873
 874 sub associate_ontology_term{
 875     my $self=shift;
 876     my $individual_id=$self->get_object_id();
 877     my $sp_person_id= $self->get_user->get_sp_person_id();
 878
 879     #   <a href=javascript:Tools.toggleAssociateOntology()>[Add ontology annotations]</a><br>
 880     my $associate = qq^
 881         <div id='associateOntForm' style="display: none">
 882             <div id='ontology_search'>
 883
 884             Ontology term:
 885                 <input type="text"
 886                        style="width: 50%"
 887                        id="ontology_input"
 888                        onkeyup="Tools.getOntologies(this.value)">
 889                 <select id = "cv_select" onchange="Tools.getOntologies(MochiKit.DOM.getElement('ontology_input').value, this.value)">
 890                        <option value="PO">PO (plant ontology)</option>
 891                        <option value="SP">SP (Solanaceae phenotypes)</option>
 892                 </select><br>
 893
 894                 <select id="ontology_select"
 895                         style="width: 100%"
 896                         name="ontology_select"
 897                         size=10
 898
 899                         onchange="Tools.getRelationship()">
 900
 901                 </select>
 902
 903                 <b>Relationship type:</b>
 904                 <select id="relationship_select" style="width: 100%"
 905                 onchange="Tools.getEvidenceCode()">
 906                 </select>
 907                 <b>Evidence code:</b>
 908                 <select id="evidence_code_select" style="width: 100%"
 909                 onchange="Tools.getEvidenceDescription();Individual.getEvidenceWith('$individual_id');Individual.getReference('$individual_id')">
 910                 </select>
 911
 912                 <b>Evidence description:</b>
 913                 <select id="evidence_description_select" style="width: 100%">
 914                 </select>
 915
 916                 <b>Evidence with:</b>
 917                 <select id="evidence_with_select" style="width: 100%">
 918                 </select>
 919
 920                 <b>Reference:</b>
 921                 <select id="reference_select" style="width: 100%">
 922                 </select>
 923
 924                 <input type="button"
 925                        id="associate_ontology_button"
 926                        value="associate ontology"
 927                        disabled="true"
 928                        onclick="Individual.associateOntology('$individual_id', '$sp_person_id');this.disabled=true;">
 929               </div>
 930         </div>
 931 ^;
 932     return $associate;
 933 }
 934