lib/CXGN/Chado/Organism.pm

   1 =head1 NAME
   2
   3 CXGN::Chado::Organism - a class to create and manipulate Chado organism objects.
   4
   5 Version:1.0
   6
   7 =head1 DESCRIPTION
   8
   9
  10 =head1 AUTHOR
  11
  12 Naama Menda <nm249@cornell.edu>
  13
  14 =cut
  15
  16 package CXGN::Chado::Organism ;
  17 use strict;
  18 use warnings;
  19 use Carp;
  20
  21 use base qw / CXGN::DB::Object / ;
  22
  23 =head2 new
  24
  25   Usage: my $organism = CXGN::Chado::Organism->new($schema, $organism_id);
  26   Desc:
  27   Ret: a CXGN::Chado::Organism object
  28   Args: a $schema a schema object,
  29         $organism_id, if $organism_id is omitted, an empty metadata object is created.
  30   Side_Effects: accesses the database, check if exists the database columns that this object use. die if the id is not an integer.
  31
  32 =cut
  33
  34 sub new {
  35     my $class = shift;
  36     my $schema = shift;
  37     my $id = shift;
  38
  39     ### First, bless the class to create the object and set the schema into the object.
  40     my $self = $class->SUPER::new($schema);
  41
  42     ##Setting sbh for using some legacy functions from the old Organism object
  43     my $dbh= $schema->storage->dbh();
  44     $self->set_dbh($dbh);
  45
  46     #Check if $id is an integer
  47     my $organism;
  48     if (defined $id) {
  49         unless ($id =~ m/^\d+$/) {  ## The id can be only an integer
  50             my $error_message = "\nDATA TYPE ERROR: The organism_id ($id) for CXGN::Chado::Organism->new() IS NOT AN INTEGER.\n\n";
  51             croak($error_message);
  52         }
  53
  54         $organism = $self->get_resultset('Organism::Organism')->find({ organism_id => $id });
  55
  56         unless (defined $organism) {
  57             my $error_message2 = "\nDATABASE COHERENCE ERROR: The organism_id ($id) for CXGN::Chado::Organism->new(\$schema, \$id) ";
  58             $error_message2 .= "DOES NOT EXIST IN THE DATABASE.\n";
  59             $error_message2 .= "If you need enforce it, you can create an empty object (my \$org = CXGN::Chado::Organism->new(\$schema)";
  60             $error_message2 .= " and set the variable (\$org->set_organism_id(\$id);)";
  61             warn($error_message2);
  62             return undef;
  63         }
  64     } else {
  65         $self->debug("Creating a new empty Organism object! " . $self->get_resultset('Organism::Organism'));
  66         $organism = $self->get_resultset('Organism::Organism')->new({});   ### Create an empty resultset object;
  67     }
  68     ###It's important to set the object row for using the accesor in other class functions
  69     $self->set_object_row($organism);
  70
  71     return $self;
  72 }
  73
  74
  75
  76 =head2 store
  77
  78  Usage: $self->store
  79  Desc:  store a new organism
  80  Ret:   a database id
  81  Args:  none
  82  Side Effects: checks if the organism exists in the database, and if does, will attempt to update
  83  Example:
  84
  85 =cut
  86
  87 sub store {
  88     my $self=shift;
  89     my $id= $self->get_organism_id();
  90     my $schema=$self->get_schema();
  91     #no organism id . Check first if genus + species exists in te database
  92     if (!$id) {
  93         my $exists= $self->exists_in_database();
  94         if (!$exists) {
  95
  96             my $new_row = $self->get_object_row();
  97             $new_row->insert();
  98
  99             $id=$new_row->organism_id();
 100
 101             $self->set_organism_id($id);
 102             $self->d(  "Inserted a new organism  " . $self->get_organism_id() ." database_id = $id\n");
 103         }else {
 104             $self->set_organism_id($exists);
 105             my $existing_organism=$self->get_resultset('Organism::Organism')->find($exists);
 106             #don't update here if organism already exist. User should call from the code exist_in_database
 107             #and instantiate a new organism object with the database organism_id
 108             #updating here is not a good idea, since it might not be what the user intended to do
 109             #and it can mess up the database.
 110
 111             $self->debug("Organism " . $self->get_species() . " " . $self->get_genus() .  " exists in database!");
 112
 113         }
 114     }else { # id exists
 115         $self->d( "Updating existing organism_id $id\n");
 116         $self->get_object_row()->update();
 117     }
 118     return $self->get_organism_id()
 119 }
 120
 121
 122 =head2 exists_in_database
 123
 124  Usage: $self->exists_in_database()
 125  Desc:  check if the genus + species exists in the organism table
 126  Ret:
 127  Args:
 128  Side Effects:
 129  Example:
 130
 131 =cut
 132
 133 sub exists_in_database {
 134     my $self=shift;
 135     my $genus= $self->get_genus() || '' ;
 136     my $species = $self->get_species() || '' ;
 137     my $o = $self->get_resultset('Organism::Organism')->search({
 138         genus  => { 'ilike' => $genus },
 139         species    => { 'ilike'  => $species  }
 140     })->single(); #  ->single() for retrieving a single row (there sould be only one genus-species entry)
 141     if ($o) { return $o->organism_id(); }
 142
 143     # search if the genus+species where set together in the species field
 144     if ($species =~ m/(.*)\s(.*)/) {
 145         $o = $self->get_resultset('Organism::Organism')->search(
 146             {
 147                 genus   => { 'ilike'=> $1 },
 148                 species => {'ilike' => $2 }
 149             })->single();
 150         if ($o) { return $o->organism_id(); }
 151     }
 152     return undef;
 153 }
 154
 155
 156 =head2 get_dbxrefs
 157
 158  Usage: $self->get_dbxrefs()
 159  Desc:  create a list of all dbxref objects associated with the organism
 160         via the organism_dbxref table
 161  Ret:   a list of CXGN::Chado::Dbxref objects
 162  Args:  none
 163  Side Effects: none
 164  Example:
 165
 166 =cut
 167
 168 sub get_dbxrefs {
 169     my $self=shift;
 170     my @organism_dbxrefs= $self->get_schema()->resultset('Organism::OrganismDbxref')->search( {organism_id => $self->get_organism_id() } );
 171
 172     my @dbxrefs=();
 173     foreach my $od (@organism_dbxrefs) {
 174         my $dbxref_id= $od->dbxref_id();
 175         push @dbxrefs, $self->get_resultset("General::Dbxref")->search( { dbxref_id => $dbxref_id } );
 176     }
 177     return  @dbxrefs;
 178 }
 179
 180
 181 =head2 add_dbxref
 182
 183  Usage: $self->add_dbxref($dbxref)
 184  Desc:  store a new organism_dbxref
 185  Ret:   database id
 186  Args:  dbxref object
 187  Side Effects: accesses the database
 188  Example:
 189
 190 =cut
 191
 192 sub add_dbxref {
 193     my $self=shift;
 194     my $dbxref=shift;
 195
 196     my $schema=$self->get_schema;
 197     my $organism_id= $self->get_organism_id();
 198     my $dbxref_id = $dbxref->get_dbxref_id();
 199     my $organism_dbxref = $schema->resultset('Organism::OrganismDbxref')->find_or_create(
 200         {
 201             organism_id => $organism_id,
 202             dbxref_id   => $dbxref_id,
 203         },
 204         );
 205     my $id = $organism_dbxref->get_column('dbxref_id');
 206     return $id;
 207 }
 208
 209
 210 =head2 add_synonym
 211
 212  Usage: $self->add_synonym($synonym)
 213  Desc:  Store a new synonym for this organism
 214  Ret:   an organismprop object
 215  Args:  a synonym (text)
 216  Side Effects: stores a new organismprop with a type_id of 'synonym'
 217  Example:
 218
 219 =cut
 220
 221 sub add_synonym {
 222     my $self=shift;
 223     my $synonym=shift;
 224
 225     my $cvterm= $self->get_resultset("Cv::Cvterm")->search( {name => 'synonym' } )->single();;
 226     my $type_id;
 227     if ($cvterm) {
 228         $type_id= $cvterm->get_column('cvterm_id');
 229         my $rank=1;
 230         my @organismprops= $self->get_schema()->resultset("Organism::Organismprop")->search(
 231             {
 232                 organism_id=>$self->get_organism_id(),
 233                 type_id =>$type_id
 234             });
 235         if (@organismprops) {
 236             my @sorted_ranks = reverse sort { $a <=> $b }  ( map($_->get_column('rank'), @organismprops) ) ;
 237             my $max_rank = $sorted_ranks[0];
 238             $rank = $max_rank+1;
 239         }
 240         my ($organismprop)= $self->get_schema()->resultset("Organism::Organismprop")->search(
 241             {
 242                 organism_id => $self->get_organism_id(),
 243                 type_id => $type_id,
 244                 value   => $synonym,
 245             });
 246         if (!$organismprop) {
 247             $organismprop= $self->get_schema()->resultset("Organism::Organismprop")->create(
 248                 {
 249                     organism_id => $self->get_organism_id(),
 250                     type_id => $type_id,
 251                     value   => $synonym,
 252                     rank  => $rank,
 253                 });
 254             return $organismprop;
 255         }
 256     }
 257     $self->d("add_synonym ERROR: 'synonym' is not a cvterm! Please update your cvterm table. a cvterm with name='synonym' is required  for storing organismprop for synonyms\n");
 258     return undef;
 259 }
 260
 261
 262 =head2 get_synonyms
 263
 264  Usage: my @synonyms= $self->get_synonyms()
 265  Desc:  find the synonyms for this organism
 266  Ret:   a list
 267  Args:  none
 268  Side Effects: get the organismprops for type_id of cvterm.name = synonym
 269  Example:
 270
 271 =cut
 272
 273 sub get_synonyms {
 274     my $self=shift;
 275     my @props= $self->get_resultset("Organism::Organismprop")->search(
 276         { organism_id => $self->get_organism_id(),
 277           type_id  => $self->get_resultset("Cv::Cvterm")->search( { name => 'synonym'} )->first()->get_column('cvterm_id')
 278         });
 279     my @synonyms;
 280     foreach my $prop (@props) {
 281         push @synonyms, $prop->get_column('value');
 282     }
 283     return @synonyms;
 284 }
 285
 286
 287
 288 =head2 get_ploidy
 289
 290  Usage: my $ploidy= $self->get_ploidy()
 291  Desc:  find the ploidy value for this organism
 292  Ret:   a scalar
 293  Args:  none
 294  Side Effects: get the organismprops for type_id of cvterm.name = ploidy
 295  Example:
 296
 297 =cut
 298
 299 sub get_ploidy {
 300     my $self=shift;
 301
 302     my $name = "ploidy";
 303     my $value = $self->get_organismprop($name);
 304     return $value;
 305 }
 306
 307
 308 =head2 get_chromosome_number
 309
 310  Usage: my $chr= $self->get_chromosome_number()
 311  Desc:  find the chromosome number  value for this organism
 312  Ret:   a scalar
 313  Args:  none
 314  Side Effects: get the organismprops for type_id of cvterm.name = chromosome_number_variation
 315  Example:
 316
 317 =cut
 318
 319 sub get_chromosome_number {
 320     my $self=shift;
 321     my $name = "chromosome_number_variation";
 322     my $value = $self->get_organismprop($name);
 323     return $value;
 324 }
 325
 326 =head2 get_genome_size
 327
 328  Usage: my $genome_size= $self->get_genome_size()
 329  Desc:  find the genome size value for this organism
 330  Ret:   a scalar
 331  Args:  none
 332  Side Effects: get the organismprops for type_id of cvterm.name = 'genome size'
 333  Example:
 334
 335 =cut
 336
 337 sub get_genome_size {
 338     my $self=shift;
 339     my $name = "genome size";
 340     my $value = $self->get_organismprop($name);
 341     return $value;
 342 }
 343
 344
 345 =head2 get_est_attribution
 346
 347  Usage: my $att= $self->get_est_attribution()
 348  Desc:  find the est attribution for this organism
 349  Ret:   a scalar
 350  Args:  none
 351  Side Effects: get the organismprops for type_id of cvterm.name = 'est attribution'
 352  Example:
 353
 354 =cut
 355
 356 sub get_est_attribution {
 357     my $self=shift;
 358     my $name= "est attribution";
 359     my $value= $self->get_organismprop($name);
 360     return $value;
 361 }
 362
 363 =head2 get_organismprop
 364
 365  Usage: $self->get_organismprop($value)
 366  Desc:  find the value of the organismprop for value $value
 367  Ret:   a string or undef
 368  Args:  $value (a cvterm name)
 369  Side Effects:
 370  Example:
 371
 372 =cut
 373
 374 sub get_organismprop {
 375     my $self=shift;
 376     my $name = shift;
 377
 378     my ($prop)= $self->get_resultset("Organism::Organismprop")->search(
 379         { organism_id => $self->get_organism_id(),
 380           type_id  => $self->get_resultset("Cv::Cvterm")->search( { name => $name } )->first()->get_column('cvterm_id')
 381         });
 382     if ($prop) {
 383         my $value= $prop->get_column('value');
 384         return $value;
 385     }
 386     return undef;
 387 }
 388
 389 =head2 get_parent
 390
 391  Usage: $self->get_parent()
 392  Desc:  get the parent organism of this object
 393  Ret:   Chado::Organism object or undef if organism has no parent (i.e. is the root in the tree)
 394  Args:  none
 395  Side Effects: accesses the phylonode table
 396  Example:
 397
 398 =cut
 399
 400 sub get_parent {
 401     my $self=shift;
 402     my $organism_id = $self->get_organism_id();
 403
 404     my ($phylonode)= $self->get_resultset("Phylogeny::PhylonodeOrganism")->search(
 405         { organism_id =>$self->get_organism_id() })->search_related('phylonode');
 406
 407     if ($phylonode) {
 408         my $parent_phylonode_id= $phylonode->get_column('parent_phylonode_id');
 409
 410         my ($parent_phylonode)= $self->get_resultset("Phylogeny::Phylonode")->search(
 411             { phylonode_id=> $parent_phylonode_id } );
 412         if ($parent_phylonode) {
 413             my ($phylonode_organism)= $self->get_resultset("Phylogeny::PhylonodeOrganism")->search(
 414                 { phylonode_id => $parent_phylonode->get_column('phylonode_id') } );
 415
 416             my $parent_organism= CXGN::Chado::Organism->new($self->get_schema(), $phylonode_organism->organism_id );
 417             return $parent_organism;
 418         }
 419     }
 420     return undef;
 421 }
 422
 423
 424 =head2 get_direct_children
 425
 426  Usage: $self->get_direct_children()
 427  Desc:  get the child organisms of this object
 428  Ret:   list of CXGN::Chado::Organism objects or an empty list if organism has no children (i.e. is a leaf in the tree)
 429  Args:  none
 430  Side Effects: accesses the phylonode table
 431  Example:
 432
 433 =cut
 434
 435 sub get_direct_children {
 436     my $self=shift;
 437     my $organism_id = $self->get_organism_id();
 438
 439     my @children=();
 440
 441     my ($phylonode)= $self->get_resultset("Phylogeny::PhylonodeOrganism")->search(
 442         { organism_id =>$self->get_organism_id() })->search_related('phylonode');
 443
 444     if ($phylonode) {
 445
 446         #my $parent_phylonode_id= $phylonode->get_column('parent_phylonode_id');
 447
 448         my @child_phylonodes = $self->get_resultset("Phylogeny::Phylonode")->search(
 449             { parent_phylonode_id => $phylonode->phylonode_id() } );
 450
 451         foreach my $d (@child_phylonodes) {
 452             my ($phylonode_organism)= $self->get_resultset("Phylogeny::PhylonodeOrganism")->search(
 453                 { phylonode_id => $d->get_column('phylonode_id') } );
 454
 455             my $child_organism= CXGN::Chado::Organism->new($self->get_schema(), $phylonode_organism->organism_id() );
 456             push @children, $child_organism;
 457         }
 458     }
 459     return @children;
 460 }
 461
 462 =head2 get_taxon
 463
 464  Usage: $sef->get_taxon()
 465  Desc:  get the taxon for this organism
 466  Ret:   a taxon name
 467  Args:  none
 468  Side Effects: looks in the phylonode table
 469  Example:
 470
 471 =cut
 472
 473 sub get_taxon {
 474     my $self = shift;
 475     my ($phylonode) = $self->get_resultset("Phylogeny::PhylonodeOrganism")->search(
 476         { organism_id=>$self->get_organism_id() } )->search_related("phylonode");
 477     if ($phylonode) {
 478         my $type_id = $phylonode->get_column('type_id');
 479
 480         my ($cvterm) = $self->get_resultset("Cv::Cvterm")->find( { cvterm_id=>$type_id });
 481         if ($cvterm) {
 482             my $taxon = $cvterm->get_column('name');
 483             return $taxon;
 484         }
 485     }
 486     return undef;
 487
 488 }
 489
 490
 491
 492
 493 #############################################
 494
 495 =head2 accessors get_species, set_species
 496
 497  Usage:
 498  Desc:
 499  Property
 500  Side Effects:
 501  Example:
 502
 503 =cut
 504
 505 sub get_species {
 506     my $self = shift;
 507     return $self->get_object_row()->get_column('species');
 508 }
 509
 510 sub set_species {
 511     my $self = shift;
 512     my $species=shift || croak " No argument passed to set_species!!!";
 513     $self->get_object_row()->set_column(species => $species ) ;
 514
 515 }
 516
 517 =head2 accessors get_genus, set_genus
 518
 519  Usage:
 520  Desc:
 521  Property
 522  Side Effects:
 523  Example:
 524
 525 =cut
 526
 527 sub get_genus {
 528     my $self = shift;
 529     return $self->get_object_row()->get_column("genus");
 530 }
 531
 532 sub set_genus {
 533     my $self = shift;
 534     $self->get_object_row()->set_column(genus => shift);
 535 }
 536
 537 =head2 accessors get_abbreviation, set_abbreviation
 538
 539  Usage:
 540  Desc:
 541  Property
 542  Side Effects:
 543  Example:
 544
 545 =cut
 546
 547 sub get_abbreviation {
 548     my $self = shift;
 549     return $self->get_object_row()->get_column("abbreviation");
 550 }
 551
 552 sub set_abbreviation {
 553     my $self = shift;
 554     $self->get_object_row()->set_column(abbreviation => shift);
 555 }
 556
 557 =head2 accessors get_common_name, set_common_name
 558
 559  Usage:
 560  Desc:
 561  Property
 562  Side Effects:
 563  Example:
 564
 565 =cut
 566
 567 sub get_common_name {
 568     my $self = shift;
 569     return $self->get_object_row()->get_column("common_name");
 570 }
 571
 572 sub set_common_name {
 573     my $self = shift;
 574     $self->get_object_row()->set_column(common_name => shift);
 575 }
 576
 577
 578 =head2 accessors get_comment, set_comment
 579
 580  Usage:
 581  Desc:
 582  Property
 583  Side Effects:
 584  Example:
 585
 586 =cut
 587
 588 sub get_comment {
 589     my $self = shift;
 590     return $self->get_object_row()->get_column("comment");
 591 }
 592
 593 sub set_comment {
 594     my $self = shift;
 595     $self->get_object_row()->set_column(comment => shift);
 596 }
 597
 598
 599
 600
 601 =head2 accessors get_organism_id, set_organism_id
 602
 603  Usage:
 604  Desc:
 605  Property
 606  Side Effects:
 607  Example:
 608
 609 =cut
 610
 611 sub get_organism_id {
 612     my $self = shift;
 613     return $self->get_object_row()->get_column('organism_id');
 614 }
 615
 616 sub set_organism_id {
 617     my $self = shift;
 618     my $organism_id=shift || croak "No argument passed to organism_id";
 619     #check if integer
 620     #check if id is in the database
 621     $self->get_object_row()->set_column(organism_id=>$organism_id);
 622 }
 623
 624
 625 sub get_object_row {
 626     my $self = shift;
 627     return $self->{object_row};
 628 }
 629
 630 sub set_object_row {
 631   my $self = shift;
 632   $self->{object_row} = shift;
 633 }
 634
 635 =head2 get_resultset
 636
 637  Usage: $self->get_resultset(ModuleName::TableName)
 638  Desc:  Get a ResultSet object for source_name
 639  Ret:   a ResultSet object
 640  Args:  a source name
 641  Side Effects: none
 642  Example:
 643
 644 =cut
 645
 646 sub get_resultset {
 647     my $self=shift;
 648     my $source = shift;
 649     return $self->get_schema()->resultset("$source");
 650 }
 651
 652
 653
 654 ###################Functions adapted from the old the organism object
 655
 656 =head2 new_with_taxon_id
 657
 658  Usage:  my $organism = CXGN::Chado::Organism->new_with_taxon_id($dbh, $gb_taxon_id)
 659  Desc:   create a new organism object using genbank taxon_id instead of organism_id
 660  Ret:    a new organism object
 661  Args:   a dbh or a dbic schema object
 662  Side Effects: creates a new Bio::Chado::Schema object
 663  Example:
 664
 665 =cut
 666
 667 sub new_with_taxon_id {
 668     my $class  = shift;
 669     my $schema = shift;
 670
 671     $schema = $class->_ensure_dbic( $schema );
 672
 673     my $taxon_id = shift;
 674
 675     my ($organism)= $schema->resultset("General::Db")->search(
 676         {  name      =>  'DB:NCBI_taxonomy' }) ->
 677         search_related('dbxrefs', { accession =>  $taxon_id } )->
 678         search_related('organism_dbxrefs')->
 679         search_related('organism');
 680     if ($organism) {
 681         return CXGN::Chado::Organism->new($schema, $organism->get_column('organism_id') );
 682     }
 683     return undef;
 684 }
 685
 686 sub _ensure_dbic {
 687     my ($self,$dbh) = @_;
 688     return $dbh if $dbh->can('resultset');
 689
 690     $dbh = $dbh->get_actual_dbh  if $dbh->isa("CXGN::DB::Connection")  ;
 691
 692     require Bio::Chado::Schema;
 693     return Bio::Chado::Schema->connect( sub { $dbh->clone },
 694                                         { on_connect_do => ['SET search_path TO public'] },
 695         );
 696
 697 }
 698
 699
 700 =head2 get_genbank_taxon_id
 701
 702  Usage:  $self->get_genbank_taxon_id
 703  Desc:   get the genbank taxon id of this organism
 704  Ret:    a string
 705  Args:
 706  Side Effects: none
 707  Example:
 708
 709 =cut
 710
 711 sub get_genbank_taxon_id {
 712     my $self = shift;
 713     my $schema= $self->get_schema();
 714     my ($db) = $schema->resultset("General::Db")->search( { name =>  'DB:NCBI_taxonomy' } );
 715     my $db_id = $db->get_column('db_id');
 716
 717     my ($dbxref)= $schema->resultset("Organism::OrganismDbxref")->search(
 718         {  organism_id => $self->get_organism_id() })->
 719         search_related('dbxref', {db_id => $db_id } ) ;
 720     my $accession = $dbxref->get_column('accession');
 721     return $accession;
 722 }
 723
 724
 725
 726 =head2 new_with_common_name
 727
 728  Usage:  my $organism = CXGN::Chado::Organism->new_with_common_name($schema, $common_name)
 729  Desc:   create a new organism object using common_name instead of organism_id
 730           Each common_name should have a 'default' organism asociated in the organismprop table
 731  Ret:    a new organism object
 732  Args:
 733  Side Effects: make a new Bio::Chado::Schema connection if $schema arg is a CXGN::DB::Connection object
 734  Example:
 735
 736 =cut
 737
 738
 739 ###Need to figure out what to do with common names
 740 sub new_with_common_name {
 741     my $self = shift;
 742     my $schema = shift;
 743     my $common_name = shift;
 744
 745     $schema = $self->_ensure_dbic( $schema );
 746
 747     my ($organism)= $schema->resultset("Cv::Cvterm")->search(
 748         {  name      =>  'common_name' }) ->
 749         search_related('organismprops', { value => $common_name } )->
 750         search_related('organism');
 751     return undef if !$organism;
 752     return CXGN::Chado::Organism->new($schema, $organism->get_column('organism_id') );
 753
 754 }
 755
 756
 757 =head2 get_intergroup_species_name DEPRECATED see get_group_common_name
 758
 759  Usage:
 760  Ret:
 761  Args:
 762  Side Effects:
 763  Example:
 764
 765 =cut
 766
 767 sub get_intergroup_species_name {
 768
 769     my $self = shift;
 770     warn "DEPRECATED. Replaced by get_group_common_name";
 771     return $self->get_group_common_name();
 772 }
 773
 774
 775
 776 =head2 get_group_common_name
 777
 778  Usage: my $group_common_name= $self->get_group_common_name()
 779  Desc:  The unigenes, loci and phenome are grouped by interspecific group class.
 780         e.g. for all tomato species we have the same number of unigene, loci or phenotypes accessions.
 781         This function  get this common_name for this organism
 782  Ret:   A string
 783  Args:
 784  Side Effects: none
 785  Example: my $species_intergroup= $organism->get_group_common_name()
 786
 787 =cut
 788
 789 sub get_group_common_name {
 790
 791     my $self = shift;
 792     my $query = "SELECT
 793                 organismgroup.name
 794                 FROM sgn.organismgroup
 795                 JOIN sgn.organismgroup_member USING (organismgroup_id)
 796                 WHERE organism_id=? AND type = ?";
 797
 798     my $sth=$self->get_dbh()->prepare($query);
 799     $sth->execute($self->get_organism_id() , 'common name');
 800
 801     my ($common_name) = $sth->fetchrow_array();
 802
 803     return $common_name;
 804
 805 }
 806
 807
 808 #############
 809 #The following methods need database changes of the organism and common_name FK
 810 #############
 811
 812
 813 =head2 get_map_data
 814
 815  Usage:  my $map_data = $self->get_map_data ();
 816  Desc:   Get the map link for an organism. The organism could be one of the parents.
 817  Ret:    array of [ map short_name , map_id ], [], ...
 818  Args:
 819  Side Effects: none
 820  Example: my ($short_name, $map_id = $organism->get_map_data();
 821
 822 =cut
 823
 824 sub get_map_data {
 825
 826     my $self = shift;
 827
 828     my $query = "SELECT DISTINCT
 829                         sgn.map.short_name,
 830                         sgn.map.map_id
 831                   FROM sgn.map
 832                   INNER JOIN sgn.accession ON (parent_1=accession_id or parent_2=accession_id or ancestor=accession_id)
 833                   INNER JOIN public.organism on  (public.organism.organism_id = sgn.accession.chado_organism_id)
 834                   WHERE public.organism.organism_id = ?";
 835
 836     my $sth=$self->get_dbh()->prepare($query);
 837     $sth->execute($self->get_organism_id() );
 838     my @map_data=();
 839
 840     while (my ($short_name, $map_id) = $sth -> fetchrow_array()) {
 841         push @map_data, [$short_name, $map_id];
 842     }
 843     return @map_data;
 844 }
 845
 846
 847 #####################
 848
 849 =head2 get_loci_count
 850
 851  Usage: my $loci_count = $self->get_loci_count();
 852  Desc:  Get the loci data for an organism  .
 853  Ret:   An integer.
 854  Args:
 855  Side Effects: none
 856  Example: my $loci_count = $organism->get_loci_count();
 857
 858 =cut
 859
 860 sub get_loci_count {
 861
 862     my $self = shift;
 863
 864     my $query = "SELECT COUNT
 865                         (phenome.locus.locus_id)
 866                  FROM phenome.locus
 867                  JOIN sgn.common_name using (common_name_id)
 868                  JOIN sgn.organismgroup  on (common_name.common_name = organismgroup.name )
 869                  JOIN sgn.organismgroup_member USING (organismgroup_id)
 870                  JOIN public.organism USING (organism_id)
 871                  WHERE locus.obsolete = 'f' AND public.organism.organism_id=?";
 872
 873     my $sth=$self->get_dbh()->prepare($query);
 874     $sth->execute($self->get_organism_id() );
 875
 876     my ($locus_count) = $sth->fetchrow_array() ;
 877     return $locus_count;
 878 }
 879
 880 =head2 get_library_list
 881
 882  Usage: my $library_count = $self->get_library_list();
 883  Desc:  Get the libraries names.
 884  Ret:  a list of library_shortnames
 885  Args:
 886  Side Effects: none
 887  Example: my $lib = $organism->get_library_list();
 888
 889 =cut
 890
 891 sub get_library_list {
 892
 893     my $self=shift;
 894
 895     my $query = "SELECT library_shortname
 896                  FROM sgn.library
 897                  JOIN public.organism on (organism.organism_id = library.chado_organism_id)
 898                  WHERE public.organism.organism_id=?";
 899     my $sth = $self->get_dbh()->prepare($query);
 900     $sth->execute($self->get_organism_id() );
 901
 902     my @libraries = ();
 903     while ( my ($library_shortname)=$sth->fetchrow_array() ) {
 904         push @libraries,  $library_shortname;
 905     }
 906     return @libraries;
 907 }
 908
 909 =head2 get_est_count
 910
 911  Usage: my $est_count = $organism->get_est_count();
 912  Desc:  Get the EST count for an organism. This number is only for the ESTs where status=0 and flags=0.
 913  Ret:   An integer.
 914  Args:
 915  Side Effects: THIS FUNCTION IS VERY SLOW. Currently not called from the organism page.
 916  Example: my $est_n = $organism->get_ests_count();
 917
 918 =cut
 919
 920 sub get_est_count {
 921
 922     my $self = shift;
 923
 924     my $query = "SELECT COUNT(
 925                         sgn.est.est_id)
 926                  FROM sgn.est
 927                  JOIN sgn.seqread USING (read_id)
 928                  JOIN sgn.clone USING (clone_id)
 929                  JOIN sgn.library USING (library_id)
 930                  JOIN public.organism ON (organism.organism_id = library.chado_organism_id)
 931                                   WHERE sgn.est.status = 0 and sgn.est.flags = 0 and public.organism.organism_id=?";
 932
 933     my $sth = $self->get_dbh()->prepare($query);
 934     $sth->execute($self->get_organism_id() );
 935     my ($est_n) = $sth->fetchrow_array() ;
 936     return $est_n;
 937 }
 938
 939 =head2 get_phenotype_count
 940
 941  Usage: my $phenotypes =$self->get_phenotype_count();
 942  Desc:  Get the phenotypes count for an organism.
 943  Ret:   An integer or undef
 944  Args:
 945  Side Effects: none
 946  Example:
 947
 948 =cut
 949
 950 sub get_phenotype_count {
 951
 952    my $self = shift;
 953
 954    my $query=" SELECT COUNT (phenome.individual.individual_id)
 955                  FROM phenome.individual
 956                  JOIN sgn.common_name using (common_name_id)
 957                  JOIN sgn.organismgroup  on (common_name.common_name = organismgroup.name )
 958                  JOIN sgn.organismgroup_member USING (organismgroup_id)
 959                  JOIN public.organism USING (organism_id)
 960                  WHERE individual.obsolete = 'f' AND public.organism.organism_id=?";
 961
 962    my $sth=$self->get_dbh()->prepare($query);
 963    $sth->execute($self->get_organism_id() );
 964
 965    my $phenotypes =0;
 966    while (my ($pheno_count) = $sth->fetchrow_array()) {
 967        $phenotypes += $pheno_count;
 968    }
 969
 970    return $phenotypes;
 971 }
 972
 973
 974 ##########################
 975
 976 =head2 get_organism_by_species
 977
 978  Usage: CXGN::Chado::Organism::get_organism_by_species($species, $schema)
 979  Desc:
 980  Ret:   Organism object or undef
 981  Args: species name and a schema object
 982  Side Effects:
 983  Example:
 984
 985 =cut
 986
 987
 988 sub get_organism_by_species {
 989     my $species=shift;
 990     my $schema= shift;
 991     my ($organism)=$schema->resultset("Organism::Organism")->find(
 992         { species => $species }
 993         ); #should be just one species...
 994
 995     return $organism || undef ;
 996 }
 997
 998
 999 =head2 get_organism_by_tax
1000
1001  Usage: $self->get_organism_by_tax($taxon)
1002  Desc:  Find the organism row for the higher level taxon of the current organism.
1003  Ret:   Organism object or undef
1004  Args:  taxon order (e.g. order, family , tribe, etc.)
1005  Side Effects:
1006  Example:
1007
1008 =cut
1009
1010
1011 sub get_organism_by_tax {
1012     my $self=shift;
1013     my $taxon=shift;
1014     my $cvterm = $self
1015         ->get_resultset("Cv::Cv")
1016         ->search({ 'me.name' => 'taxonomy'})
1017         ->search_related('cvterms', {
1018             'cvterms.name'   => $taxon,
1019             is_obsolete => 0,
1020           })
1021         ->single;
1022
1023     if( $cvterm ) {
1024
1025         my $type_id = $cvterm->get_column('cvterm_id');
1026
1027         my ($self_phylonode)= $self->get_resultset("Phylogeny::PhylonodeOrganism")->search(
1028             { organism_id => $self->get_organism_id() } )->search_related('phylonode');
1029         if ($self_phylonode) {
1030             my $left_idx= $self_phylonode->get_column('left_idx');
1031             my $right_idx=$self_phylonode->get_column('right_idx');
1032             my ($phylonode)=$self->get_resultset("Phylogeny::Phylonode")->search_literal(
1033                 ('left_idx < ? AND right_idx > ? AND type_id = ?' , ($left_idx, $right_idx, $type_id) ));
1034
1035             if ($phylonode) {
1036                 my ($organism)= $self->get_resultset("Phylogeny::PhylonodeOrganism")->search(
1037                     { phylonode_id => $phylonode->get_column('phylonode_id') } )->search_related('organism');
1038
1039                 return $organism || undef ;
1040             }
1041         } else { warn("NO PHYLONODE stored for organism " . $self->get_abbreviation() . "\n");  }
1042     } else {  warn("NO CVTERM FOUND for term '$taxon'!! Check your database\n"); }
1043
1044     return;
1045 }
1046
1047 =head2 new_with_species
1048
1049  Usage: my $o=CXGN::Chado::Organism->new_with_species($schema, 'my node name')
1050  Desc:  Instantiate a new organism object with species name.
1051         species name is anything that is stored in the species column
1052         which means it does not have to be a taxonmic species, but can be any tax name,
1053         as long as it is unique.
1054  Ret:   an organism object
1055  Args:  Bio::Chado::Schema object and a string
1056  Side Effects:
1057  Example:
1058
1059 =cut
1060
1061 sub new_with_species {
1062     my $self=shift;
1063     my $schema= shift;
1064     my $species=shift;
1065     my ($organism) = $schema->resultset('Organism::Organism')->search(
1066         { species => $species }
1067         );
1068     if ($organism) {
1069         my $o = CXGN::Chado::Organism->new($schema, $organism->get_column('organism_id') );
1070         return $o;
1071     }
1072     return undef;
1073 }
1074 =head2 has_avail_genome
1075
1076  Usage: my $o=CXGN::Chado::Organism->new()
1077         my $hasgenome = $o->has_avail_genome();
1078  Desc:  Return 'yes' if organism has an available genome information; 'no' otherwise.
1079  Ret:   a string
1080  Args:  None
1081  Side Effects:
1082  Example:
1083
1084 =cut
1085 sub has_avail_genome{
1086     my $self= shift;
1087     my $avail_genome;
1088
1089     if (defined($self->get_ploidy()) ||defined( $self->get_genome_size()) || defined($self->get_chromosome_number())){
1090         $avail_genome= 'yes';
1091           } else {
1092            $avail_genome= 'no';
1093           }
1094     return $avail_genome;
1095 }
1096 =head2 has_avail_map
1097
1098  Usage: my $o=CXGN::Chado::Organism->new()
1099         my $hasmap = $o->has_avail_map();
1100  Desc:  Return 'yes' if organism has an available map; 'no' otherwise.
1101  Ret:   a string
1102  Args:  None
1103  Side Effects:
1104  Example:
1105
1106 =cut
1107
1108 sub has_avail_map{
1109     my $self = shift;
1110     my $avail_map;
1111     if(defined($self->get_map_data())){
1112        $avail_map = 'yes';
1113         } else {
1114          $avail_map = 'no';
1115       }
1116     return $avail_map;
1117 }
1118 1;
1119