lib/CXGN/Stock/Accession.pm

   1
   2 =head1 NAME
   3
   4 CXGN::Stock::Accession - a class to represent accessions in the database
   5
   6 =head1 DESCRIPTION
   7
   8
   9 CXGN::Stock::Accession inherits from CXGN::Stock. The required fields are:
  10
  11 uniquename
  12
  13 Code structure copied from CXGN::Stock::Seedlot, with inheritance from CXGN::Stock
  14
  15 =head1 AUTHOR
  16
  17
  18 =head1 ACCESSORS & METHODS
  19
  20 =cut
  21
  22 package CXGN::Stock::Accession;
  23
  24 use Moose;
  25 use JSON;
  26
  27 extends 'CXGN::Stock';
  28
  29 use Data::Dumper;
  30 use CXGN::BreedersToolbox::Projects;
  31 use SGN::Model::Cvterm;
  32
  33 has 'owner_sp_person' => (
  34     isa => 'ArrayRef',
  35     is => 'rw',
  36     lazy    => 1,
  37     builder => '_build_owner_sp_person',
  38 );
  39
  40 has 'main_production_site_url' => (
  41     isa => 'Str',
  42     is => 'rw',
  43 );
  44
  45 has 'accessionNumber' => (
  46     isa => 'Maybe[Str]',
  47     is => 'rw',
  48     lazy     => 1,
  49     builder  => '_retrieve_accessionNumber',
  50 );
  51
  52 has 'germplasmPUI' => (
  53     isa => 'Maybe[Str]',
  54     is => 'rw',
  55     lazy     => 1,
  56     builder  => '_retrieve_germplasmPUI',
  57 );
  58
  59 has 'pedigree' => (
  60     isa => 'Maybe[Str]',
  61     is => 'rw',
  62 );
  63
  64 has 'mother_accession' => (
  65     isa => 'Maybe[Str]',
  66     is  => 'rw',
  67 );
  68
  69 has 'father_accession' => (
  70     isa => 'Maybe[Str]',
  71     is  => 'rw',
  72 );
  73
  74 has 'additional_info' => (
  75     isa => 'Maybe[HashRef]',
  76     is => 'rw'
  77 );
  78
  79 has 'germplasmSeedSource' => (
  80     isa => 'Maybe[Str]',
  81     is => 'rw',
  82     lazy     => 1,
  83     builder  => '_retrieve_germplasmSeedSource',
  84 );
  85
  86 has 'synonyms' => (
  87     isa => 'Maybe[ArrayRef[Str]]',
  88     is => 'rw',
  89     lazy     => 1,
  90     builder  => '_retrieve_synonyms',
  91 );
  92
  93 has 'instituteCode' => (
  94     isa => 'Maybe[Str]',
  95     is => 'rw',
  96     lazy     => 1,
  97     builder  => '_retrieve_instituteCode',
  98 );
  99
 100 has 'instituteName' => (
 101     isa => 'Maybe[Str]',
 102     is => 'rw',
 103     lazy     => 1,
 104     builder  => '_retrieve_instituteName',
 105 );
 106
 107 has 'biologicalStatusOfAccessionCode' => (
 108     isa => 'Maybe[Str]',
 109     is => 'rw',
 110     lazy     => 1,
 111     builder  => '_retrieve_biologicalStatusOfAccessionCode',
 112 );
 113
 114 has 'countryOfOriginCode' => (
 115     isa => 'Maybe[Str]',
 116     is => 'rw',
 117     lazy     => 1,
 118     builder  => '_retrieve_countryOfOriginCode',
 119 );
 120
 121 has 'typeOfGermplasmStorageCode' => (
 122     isa => 'Maybe[Str]',
 123     is => 'rw',
 124     lazy     => 1,
 125     builder  => '_retrieve_typeOfGermplasmStorageCode',
 126 );
 127
 128 has 'donors' => (
 129     isa => 'Maybe[ArrayRef[HashRef]]',
 130     is => 'rw',
 131     lazy     => 1,
 132     builder  => '_retrieve_donors',
 133 );
 134
 135 has 'acquisitionDate' => (
 136     isa => 'Maybe[Str]',
 137     is => 'rw',
 138     lazy     => 1,
 139     builder  => '_retrieve_acquisitionDate',
 140 );
 141
 142 has 'entryNumber' => (
 143     isa => 'Maybe[Str]',
 144     is => 'rw',
 145     lazy     => 1,
 146     builder  => '_retrieve_entryNumber',
 147 );
 148
 149 has 'variety' => (
 150     isa => 'Maybe[Str]',
 151     is => 'rw',
 152     lazy     => 1,
 153     builder  => '_retrieve_variety',
 154 );
 155
 156 has 'state' => (
 157     isa => 'Maybe[Str]',
 158     is => 'rw',
 159     lazy     => 1,
 160     builder  => '_retrieve_state',
 161 );
 162
 163 has 'notes' => (
 164     isa => 'Maybe[Str]',
 165     is => 'rw',
 166     lazy     => 1,
 167     builder  => '_retrieve_notes',
 168 );
 169
 170 has 'locationCode' => (
 171     isa => 'Maybe[Str]',
 172     is => 'rw',
 173     lazy     => 1,
 174     builder  => '_retrieve_location_code',
 175 );
 176
 177 has 'ploidyLevel' => (
 178     isa => 'Maybe[Str]',
 179     is => 'rw',
 180     lazy     => 1,
 181     builder  => '_retrieve_ploidy_level',
 182 );
 183
 184 has 'genomeStructure' => (
 185     isa => 'Maybe[Str]',
 186     is => 'rw',
 187     lazy     => 1,
 188     builder  => '_retrieve_genome_structure',
 189 );
 190
 191 has 'transgenic' => (
 192     isa => 'Maybe[Str]',
 193     is => 'rw',
 194     lazy     => 1,
 195     builder  => '_retrieve_transgenic',
 196 );
 197
 198 has 'introgression_parent' => (
 199     isa => 'Maybe[Str]',
 200     is => 'rw',
 201     lazy     => 1,
 202     builder  => '_retrieve_introgression_parent',
 203 );
 204
 205 has 'introgression_backcross_parent' => (
 206     isa => 'Maybe[Str]',
 207     is => 'rw',
 208     lazy     => 1,
 209     builder  => '_retrieve_introgression_backcross_parent',
 210 );
 211
 212 has 'introgression_map_version' => (
 213     isa => 'Maybe[Str]',
 214     is => 'rw',
 215     lazy     => 1,
 216     builder  => '_retrieve_introgression_map_version',
 217 );
 218
 219 has 'introgression_chromosome' => (
 220     isa => 'Maybe[Str]',
 221     is => 'rw',
 222     lazy     => 1,
 223     builder  => '_retrieve_introgression_chromosome',
 224 );
 225
 226 has 'introgression_start_position_bp' => (
 227     isa => 'Maybe[Str]',
 228     is => 'rw',
 229     lazy     => 1,
 230     builder  => '_retrieve_introgression_start_position_bp',
 231 );
 232
 233 has 'introgression_end_position_bp' => (
 234     isa => 'Maybe[Str]',
 235     is => 'rw',
 236     lazy     => 1,
 237     builder  => '_retrieve_introgression_end_position_bp',
 238 );
 239
 240 has 'other_editable_stock_props' => (
 241     isa => 'Maybe[HashRef]',
 242     is => 'rw'
 243 );
 244
 245 sub BUILD {
 246     my $self = shift;
 247
 248 }
 249
 250 sub _retrieve_germplasmPUI {
 251     my $self = shift;
 252     $self->germplasmPUI($self->_retrieve_stockprop('PUI'));
 253 }
 254
 255 sub _retrieve_accessionNumber {
 256     my $self = shift;
 257     $self->accessionNumber($self->_retrieve_stockprop('accession number'));
 258 }
 259
 260 sub _retrieve_germplasmSeedSource {
 261     my $self = shift;
 262     $self->germplasmSeedSource($self->_retrieve_stockprop('seed source'));
 263 }
 264
 265 sub _retrieve_synonyms {
 266     my $self = shift;
 267     my @synonyms = $self->_retrieve_stockprop('stock_synonym') ? split ',', $self->_retrieve_stockprop('stock_synonym') : ();
 268     $self->synonyms(\@synonyms);
 269 }
 270
 271 sub _retrieve_instituteCode {
 272     my $self = shift;
 273     $self->instituteCode($self->_retrieve_stockprop('institute code'));
 274 }
 275
 276 sub _retrieve_instituteName {
 277     my $self = shift;
 278     $self->instituteName($self->_retrieve_stockprop('institute name'));
 279 }
 280
 281 sub _retrieve_entryNumber {
 282     my $self = shift;
 283     $self->entryNumber($self->_retrieve_stockprop('entry number'));
 284 }
 285
 286 sub _retrieve_variety {
 287     my $self = shift;
 288     $self->variety($self->_retrieve_stockprop('variety'));
 289 }
 290
 291 sub _retrieve_state {
 292     my $self = shift;
 293     $self->state($self->_retrieve_stockprop('state'));
 294 }
 295
 296 sub _retrieve_biologicalStatusOfAccessionCode {
 297     my $self = shift;
 298     $self->biologicalStatusOfAccessionCode($self->_retrieve_stockprop('biological status of accession code'));
 299 }
 300
 301 sub _retrieve_countryOfOriginCode {
 302     my $self = shift;
 303     $self->countryOfOriginCode($self->_retrieve_stockprop('country of origin'));
 304 }
 305
 306 sub _retrieve_typeOfGermplasmStorageCode {
 307     my $self = shift;
 308     $self->typeOfGermplasmStorageCode($self->_retrieve_stockprop('type of germplasm storage code'));
 309 }
 310
 311 sub _retrieve_acquisitionDate {
 312     my $self = shift;
 313     $self->acquisitionDate($self->_retrieve_stockprop('acquisition date'));
 314 }
 315
 316 sub _retrieve_donors {
 317     my $self = shift;
 318     my @donor_accessions = $self->_retrieve_stockprop('donor') ? split ',', $self->_retrieve_stockprop('donor') : ();
 319     my @donor_institutes = $self->_retrieve_stockprop('donor institute') ? split ',', $self->_retrieve_stockprop('donor institute') : ();
 320     my @donor_puis = $self->_retrieve_stockprop('donor PUI') ? split ',', $self->_retrieve_stockprop('donor PUI') : ();
 321     my @donor_array;
 322     if (scalar(@donor_accessions)>0 && scalar(@donor_institutes)>0 && scalar(@donor_puis)>0 && scalar(@donor_accessions) == scalar(@donor_institutes) && scalar(@donor_accessions) == scalar(@donor_puis)){
 323         for (0 .. scalar(@donor_accessions)-1){
 324             push @donor_array, {
 325                 'donorGermplasmName'=>$donor_accessions[$_],
 326                 'donorAccessionNumber'=>$donor_accessions[$_],
 327                 'donorInstituteCode'=>$donor_institutes[$_],
 328                 'germplasmPUI'=>$donor_puis[$_]
 329             };
 330         }
 331     }
 332     $self->donors(\@donor_array);
 333 }
 334
 335 sub _retrieve_notes {
 336     my $self = shift;
 337     $self->notes($self->_retrieve_stockprop('notes'));
 338 }
 339
 340 sub _retrieve_location_code {
 341     my $self = shift;
 342     $self->locationCode($self->_retrieve_stockprop('location_code'));
 343 }
 344
 345 sub _retrieve_ploidy_level {
 346     my $self = shift;
 347     $self->ploidyLevel($self->_retrieve_stockprop('ploidy_level'));
 348 }
 349
 350 sub _retrieve_genome_structure {
 351     my $self = shift;
 352     $self->genomeStructure($self->_retrieve_stockprop('genome_structure'));
 353 }
 354
 355 sub _retrieve_transgenic {
 356     my $self = shift;
 357     $self->transgenic($self->_retrieve_stockprop('transgenic'));
 358 }
 359
 360 sub _retrieve_introgression_parent {
 361     my $self = shift;
 362     $self->introgression_parent($self->_retrieve_stockprop('introgression_parent'));
 363 }
 364
 365 sub _retrieve_introgression_backcross_parent {
 366     my $self = shift;
 367     $self->introgression_backcross_parent($self->_retrieve_stockprop('introgression_backcross_parent'));
 368 }
 369
 370 sub _retrieve_introgression_map_version {
 371     my $self = shift;
 372     $self->introgression_map_version($self->_retrieve_stockprop('introgression_map_version'));
 373 }
 374
 375 sub _retrieve_introgression_chromosome {
 376     my $self = shift;
 377     $self->introgression_chromosome($self->_retrieve_stockprop('introgression_chromosome'));
 378 }
 379
 380 sub _retrieve_introgression_start_position_bp {
 381     my $self = shift;
 382     $self->introgression_start_position_bp($self->_retrieve_stockprop('introgression_start_position_bp'));
 383 }
 384
 385 sub _retrieve_introgression_end_position_bp {
 386     my $self = shift;
 387     $self->introgression_end_position_bp($self->_retrieve_stockprop('introgression_end_position_bp'));
 388 }
 389
 390 =head2 store()
 391
 392  Usage:        my $stock_id = $accession->store();
 393  Desc:         stores the current state of the object to the db
 394  Ret:          the created stock id.
 395  Args:         none
 396  Side Effects:
 397  Example:
 398
 399 =cut
 400
 401 sub store {
 402     my $self = shift;
 403
 404     print STDERR "storing: UNIQUENAME=".$self->uniquename()."\n";
 405
 406     my $id = $self->SUPER::store();
 407
 408     if ($self->accessionNumber){
 409         $self->_update_stockprop('accession number', $self->accessionNumber);
 410     }
 411
 412     #Include the newly created entry in this database as a PUI
 413     my @germplasm_pui = ($self->main_production_site_url."/stock/".$id."/view");
 414     if ($self->germplasmPUI){
 415         push @germplasm_pui, $self->germplasmPUI;
 416     }
 417     $self->_update_stockprop('PUI', join(',',@germplasm_pui));
 418
 419     if ($self->germplasmSeedSource){
 420         $self->_update_stockprop('seed source', $self->germplasmSeedSource);
 421     }
 422     # Delete synonyms
 423     $self->_remove_stockprop_all_of_type('stock_synonym');
 424     # Reinsert
 425     if ($self->synonyms){
 426         $self->_store_stockprop('stock_synonym', join(',', @{ $self->synonyms }));
 427     }
 428     if ($self->instituteCode){
 429         $self->_update_stockprop('institute code', $self->instituteCode);
 430     }
 431     if ($self->instituteName){
 432         $self->_update_stockprop('institute name', $self->instituteName);
 433     }
 434     if ($self->biologicalStatusOfAccessionCode){
 435         $self->_update_stockprop('biological status of accession code', $self->biologicalStatusOfAccessionCode);
 436     }
 437     if ($self->countryOfOriginCode){
 438         $self->_update_stockprop('country of origin', $self->countryOfOriginCode);
 439     }
 440     if ($self->typeOfGermplasmStorageCode){
 441         $self->_update_stockprop('type of germplasm storage code', $self->typeOfGermplasmStorageCode);
 442     }
 443     if ($self->acquisitionDate){
 444         $self->_update_stockprop('acquisition date', $self->acquisitionDate);
 445     }
 446     if ($self->donors){
 447         $self->_remove_stockprop_all_of_type('donor');
 448         $self->_remove_stockprop_all_of_type('donor institute');
 449         $self->_remove_stockprop_all_of_type('donor PUI');
 450         foreach (@{$self->donors}){
 451             my $accession = $_->{donorAccessionNumber} || $_->{donorGermplasmName};
 452             $self->_store_stockprop('donor', $accession);
 453             $self->_store_stockprop('donor institute', $_->{donorInstituteCode});
 454             $self->_store_stockprop('donor PUI', $_->{germplasmPUI});
 455         }
 456     }
 457     $self->_remove_parent_relationship('female_parent');
 458     if ($self->mother_accession) {
 459         my $return = $self->_store_parent_relationship('female_parent', $self->mother_accession, 'biparental');
 460         # TODO: delete accession if error and return error
 461     }
 462     $self->_remove_parent_relationship('male_parent');
 463     if ($self->father_accession) {
 464         my $return = $self->_store_parent_relationship('male_parent', $self->father_accession, 'biparental');
 465         # TODO: delete accession if error and return error
 466     }
 467     if ($self->additional_info) {
 468         $self->_update_stockprop('stock_additional_info', encode_json $self->additional_info);
 469     }
 470
 471     if($self->pedigree){
 472         print STDERR "CXGN::Stock::Accession->store does not store pedigree info yet!\n";
 473     }
 474     if ($self->variety){
 475         $self->_update_stockprop('variety', $self->variety);
 476     }
 477     if ($self->state){
 478         $self->_update_stockprop('state', $self->state);
 479     }
 480     if ($self->notes){
 481         $self->_update_stockprop('notes', $self->notes);
 482     }
 483     if ($self->locationCode){
 484         $self->_update_stockprop('location_code', $self->locationCode);
 485     }
 486     if ($self->ploidyLevel){
 487         $self->_update_stockprop('ploidy_level', $self->ploidyLevel);
 488     }
 489     if ($self->genomeStructure){
 490         $self->_update_stockprop('genome_structure', $self->genomeStructure);
 491     }
 492     if ($self->transgenic){
 493         $self->_update_stockprop('transgenic', $self->transgenic);
 494     }
 495     if ($self->introgression_parent){
 496         $self->_update_stockprop('introgression_parent', $self->introgression_parent);
 497     }
 498     if ($self->introgression_backcross_parent){
 499         $self->_update_stockprop('introgression_backcross_parent', $self->introgression_backcross_parent);
 500     }
 501     if ($self->introgression_map_version){
 502         $self->_update_stockprop('introgression_map_version', $self->introgression_map_version);
 503     }
 504     if ($self->introgression_chromosome){
 505         $self->_update_stockprop('introgression_chromosome', $self->introgression_chromosome);
 506     }
 507     if ($self->introgression_start_position_bp){
 508         $self->_update_stockprop('introgression_start_position_bp', $self->introgression_start_position_bp);
 509     }
 510     if ($self->introgression_end_position_bp){
 511         $self->_update_stockprop('introgression_end_position_bp', $self->introgression_end_position_bp);
 512     }
 513     if ($self->other_editable_stock_props){
 514         while (my ($key, $value) = each %{$self->other_editable_stock_props}) {
 515
 516             # For other_editable_stock_props that can come from accession file upload and are defined in the editable_stock_props configuration
 517             my $q = "SELECT t.cvterm_id FROM cvterm as t JOIN cv ON(t.cv_id=cv.cv_id) WHERE t.name=? and cv.name=?;";
 518             my $h = $self->schema->storage->dbh()->prepare($q);
 519             $h->execute($key, 'stock_property');
 520             my ($cvterm_id) = $h->fetchrow_array();
 521             if (!$cvterm_id) {
 522                 my $new_term = $self->schema->resultset("Cv::Cvterm")->create_with({
 523                    name => $key,
 524                    cv => 'stock_property'
 525                 });
 526                 $cvterm_id = $new_term->cvterm_id();
 527             }
 528
 529             $self->_update_stockprop($key, $value);
 530         }
 531     }
 532
 533     print STDERR "Saving returned ID $id.\n";
 534     $self->stock_id($id);
 535
 536     return $self->stock_id();
 537 }
 538
 539
 540 no Moose;
 541 __PACKAGE__->meta->make_immutable;
 542
 543 1;
 544