lib/CXGN/Chado/Stock.pm

   1 =head1 NAME
   2
   3 CXGN::Chado::Stock - a second-level DBIC Bio::Chado::Schema::Stock::Stock object
   4
   5 Version:1.0
   6
   7 =head1 DESCRIPTION
   8
   9 Created to work with  CXGN::Page::Form::AjaxFormPage
  10 for eliminating the need to refactor the  AjaxFormPage and Editable  to work with DBIC objects.
  11 Functions such as 'get_obsolete' , 'store' , and 'exists_in_database' are required , and do not use standard DBIC syntax.
  12
  13 =head1 AUTHOR
  14
  15 Naama Menda <nm249@cornell.edu>
  16
  17 =cut
  18
  19 package CXGN::Chado::Stock ;
  20 use strict;
  21 use warnings;
  22 use Carp;
  23 use Bio::Chado::Schema;
  24 use CXGN::Metadata::Schema;
  25
  26 use base qw / CXGN::DB::Object / ;
  27
  28 =head2 new
  29
  30   Usage: my $stock = CXGN::Chado::Stock->new($schema, $stock_id);
  31   Desc:
  32   Ret: a CXGN::Chado::Stock object
  33   Args: a $schema a schema object,
  34         $stock_id, if omitted, an empty stock object is created.
  35   Side_Effects: accesses the database, check if exists the database columns that this object use. die if the id is not an integer.
  36
  37 =cut
  38
  39 sub new {
  40     my $class = shift;
  41     my $schema = shift;
  42     my $id = shift;
  43
  44      ### First, bless the class to create the object and set the schema into the object.
  45     #my $self = $class->SUPER::new($schema);
  46     my $self = bless {}, $class;
  47     $self->set_schema($schema);
  48     my $stock;
  49     if (defined $id) {
  50         $stock = $self->get_resultset('Stock::Stock')->find({ stock_id => $id });
  51     } else {
  52         ### Create an empty resultset object;
  53         $stock = $self->get_resultset('Stock::Stock')->new( {} );
  54     }
  55     ###It's important to set the object row for using the accesor in other class functions
  56     $self->set_object_row($stock);
  57     return $self;
  58 }
  59
  60
  61
  62 =head2 store
  63
  64  Usage: $self->store
  65  Desc:  store a new stock
  66  Ret:   a database id
  67  Args:  none
  68  Side Effects: checks if the stock exists in the database, and if does, will attempt to update
  69  Example:
  70
  71 =cut
  72
  73 sub store {
  74     my $self=shift;
  75     my $id = $self->get_stock_id();
  76     my $schema=$self->get_schema();
  77     #no stock id . Check first if the name  exists in te database
  78     if (!$id) {
  79         my $exists= $self->exists_in_database();
  80         if (!$exists) {
  81             my $new_row = $self->get_object_row();
  82             $new_row->insert();
  83
  84             $id=$new_row->stock_id();
  85         }else {
  86             my $existing_stock=$self->get_resultset('Stock::Stock')->find($exists);
  87             #don't update here if stock already exist. User should call from the code exist_in_database
  88             #and instantiate a new stock object with the database id
  89             #updating here is not a good idea, since it might not be what the user intended to do
  90             #and it can mess up the database.
  91         }
  92     }else { # id exists
  93         $self->get_object_row()->update();
  94     }
  95     return $id
  96 }
  97
  98 ########################
  99
 100
 101 =head2 exists_in_database
 102
 103  Usage: $self->exists_in_database()
 104  Desc:  check if the uniquename exists in the stock table
 105  Ret:
 106  Args:
 107  Side Effects:
 108  Example:
 109
 110 =cut
 111
 112 sub exists_in_database {
 113     my $self=shift;
 114     my $stock_id = $self->get_stock_id();
 115     my $uniquename = $self->get_uniquename || '' ;
 116     my ($s) = $self->get_resultset('Stock::Stock')->search(
 117         {
 118             uniquename  => { 'ilike' => $uniquename },
 119         });
 120     #loading new stock - $stock_id is undef
 121     if (defined($s) && !$stock_id ) {  return $s->stock_id ; }
 122
 123     #updating an existing stock
 124     elsif ($stock_id && defined($s) ) {
 125         if ( ($s->stock_id == $stock_id) ) {
 126             return 0;
 127             #trying to update the uniquename
 128         } elsif ( $s->stock_id != $stock_id ) {
 129             return " Can't update an existing stock $stock_id uniquename:$uniquename.";
 130             # if the new name we're trying to update/insert does not exist in the stock table..
 131         } elsif ($stock_id && !$s->stock_id) {
 132             return 0;
 133         }
 134     }
 135     return undef;
 136 }
 137
 138 =head2 get_organism
 139
 140  Usage: $self->get_organism
 141  Desc:  find the organism object of this stock
 142  Ret:   L<Bio::Chado::Schema::Organism::Organism> object
 143  Args:  none
 144  Side Effects: none
 145  Example:
 146
 147 =cut
 148
 149 sub get_organism {
 150     my $self = shift;
 151     if (my $bcs_stock = $self->get_object_row) {
 152         return $bcs_stock->organism;
 153     }
 154     return undef;
 155 }
 156
 157 =head2 get_type
 158
 159  Usage: $self->get_type
 160  Desc:  find the cvterm type of this stock
 161  Ret:   L<Bio::Chado::Schema::Cv::Cvterm> object
 162  Args:   none
 163  Side Effects: none
 164  Example:
 165
 166 =cut
 167
 168 sub get_type {
 169     my $self = shift;
 170
 171     if (my $bcs_stock = $self->get_object_row ) {
 172         return  $bcs_stock->type;
 173     }
 174     return undef;
 175
 176 }
 177
 178
 179
 180 sub get_object_row {
 181     my $self = shift;
 182     return $self->{object_row};
 183 }
 184
 185 sub set_object_row {
 186   my $self = shift;
 187   $self->{object_row} = shift;
 188 }
 189
 190 =head2 get_resultset
 191
 192  Usage: $self->get_resultset(ModuleName::TableName)
 193  Desc:  Get a ResultSet object for source_name
 194  Ret:   a ResultSet object
 195  Args:  a source name
 196  Side Effects: none
 197  Example:
 198
 199 =cut
 200
 201 sub get_resultset {
 202     my $self=shift;
 203     my $source = shift;
 204     return $self->get_schema()->resultset("$source");
 205 }
 206
 207 =head2 accessors get_schema, set_schema
 208
 209  Usage:
 210  Desc:
 211  Property
 212  Side Effects:
 213  Example:
 214
 215 =cut
 216
 217 sub get_schema {
 218   my $self = shift;
 219   return $self->{schema};
 220 }
 221
 222 sub set_schema {
 223   my $self = shift;
 224   $self->{schema} = shift;
 225 }
 226
 227
 228 ###mapping accessors to DBIC
 229
 230 =head2 accessors get_name, set_name
 231
 232  Usage:
 233  Desc:
 234  Property
 235  Side Effects:
 236  Example:
 237
 238 =cut
 239
 240 sub get_name {
 241     my $self = shift;
 242     return $self->get_object_row()->get_column("name");
 243 }
 244
 245 sub set_name {
 246     my $self = shift;
 247     $self->get_object_row()->set_column(name => shift);
 248 }
 249
 250 =head2 accessors get_uniquename, set_uniquename
 251
 252  Usage:
 253  Desc:
 254  Property
 255  Side Effects:
 256  Example:
 257
 258 =cut
 259
 260 sub get_uniquename {
 261     my $self = shift;
 262     return $self->get_object_row()->get_column("uniquename");
 263 }
 264
 265 sub set_uniquename {
 266     my $self = shift;
 267     $self->get_object_row()->set_column(uniquename => shift);
 268 }
 269
 270 =head2 accessors get_organism_id, set_organism_id
 271
 272  Usage:
 273  Desc:
 274  Property
 275  Side Effects:
 276  Example:
 277
 278 =cut
 279
 280 sub get_organism_id {
 281     my $self = shift;
 282     if (my $bcs_stock =  $self->get_object_row ) {
 283         return $bcs_stock->get_column("organism_id");
 284     }
 285     return undef;
 286 }
 287
 288 sub set_organism_id {
 289     my $self = shift;
 290     $self->get_object_row()->set_column(organism_id => shift);
 291 }
 292
 293 =head2 accessors get_type_id, set_type_id
 294
 295  Usage:
 296  Desc:
 297  Property
 298  Side Effects:
 299  Example:
 300
 301 =cut
 302
 303 sub get_type_id {
 304     my $self = shift;
 305     if (my $bcs_stock = $self->get_object_row ) {
 306         return $bcs_stock->get_column("type_id");
 307     }
 308 }
 309
 310 sub set_type_id {
 311     my $self = shift;
 312     $self->get_object_row()->set_column(type_id => shift);
 313 }
 314
 315 =head2 accessors get_description, set_description
 316
 317  Usage:
 318  Desc:
 319  Property
 320  Side Effects:
 321  Example:
 322
 323 =cut
 324
 325 sub get_description {
 326     my $self = shift;
 327     return $self->get_object_row()->get_column("description");
 328 }
 329
 330 sub set_description {
 331     my $self = shift;
 332     $self->get_object_row()->set_column(description => shift);
 333 }
 334
 335 =head2 accessors get_stock_id, set_stock_id
 336
 337  Usage:
 338  Desc:
 339  Property
 340  Side Effects:
 341  Example:
 342
 343 =cut
 344
 345 sub get_stock_id {
 346     my $self = shift;
 347     if ( my $bcs_stock = $self->get_object_row ) {
 348         return $bcs_stock->get_column("stock_id");
 349     }
 350     return undef;
 351 }
 352
 353 sub set_stock_id {
 354     my $self = shift;
 355     $self->get_object_row()->set_column(stock_id => shift);
 356 }
 357
 358 =head2 accessors get_is_obsolete, set_is_obsolete
 359
 360  Usage:
 361  Desc:
 362  Property
 363  Side Effects:
 364  Example:
 365
 366 =cut
 367
 368 sub get_is_obsolete {
 369     my $self = shift;
 370     my $stock = $self->get_object_row();
 371     return $stock->get_column("is_obsolete") if $stock;
 372 }
 373
 374 sub set_is_obsolete {
 375     my $self = shift;
 376     $self->get_object_row()->set_column(is_obsolete => shift);
 377 }
 378
 379 =head2 function get_image_ids
 380
 381   Synopsis:     my @images = $self->get_image_ids()
 382   Arguments:    none
 383   Returns:      a list of image ids
 384   Side effects: none
 385   Description:  a method for fetching all images associated with a stock
 386
 387 =cut
 388
 389 sub get_image_ids {
 390     my $self = shift;
 391     my $ids = $self->get_schema->storage->dbh->selectcol_arrayref
 392         ( "SELECT image_id FROM phenome.stock_image WHERE stock_id=? ",
 393           undef,
 394           $self->get_stock_id
 395         );
 396     return @$ids;
 397 }
 398
 399 =head2 associate_allele
 400
 401  Usage: $self->associate_allele($allele_id, $sp_person_id)
 402  Desc:  store a stock-allele link in phenome.stock_allele
 403  Ret:   a database id
 404  Args:  allele_id, sp_person_id
 405  Side Effects:  store a metadata row
 406  Example:
 407
 408 =cut
 409
 410 sub associate_allele {
 411     my $self = shift;
 412     my $allele_id = shift;
 413     my $sp_person_id = shift;
 414     if (!$allele_id || !$sp_person_id) {
 415         warn "Need both allele_id and person_id for linking the stock with an allele!";
 416         return
 417     }
 418     my $metadata_schema = CXGN::Metadata::Schema->connect(
 419         sub { $self->get_schema->storage->dbh },
 420         { on_connect_do => ['SET search_path TO metadata;'] },
 421         );
 422     my $metadata = CXGN::Metadata::Metadbdata->new($metadata_schema);
 423     $metadata->set_create_person_id($sp_person_id);
 424     my $metadata_id = $metadata->store()->get_metadata_id();
 425     #check if the allele is already linked
 426     my $ids =  $self->get_schema->storage->dbh->selectcol_arrayref
 427         ( "SELECT stock_allele_id FROM phenome.stock_allele WHERE stock_id = ? AND allele_id = ?",
 428           undef,
 429           $self->get_stock_id,
 430           $allele_id
 431         );
 432     if ($ids) { warn "Allele $allele_id is already linked with stock " . $self->get_stock_id ; }
 433 #store the allele_id - stock_id link
 434     my $q = "INSERT INTO phenome.stock_allele (stock_id, allele_id, metadata_id) VALUES (?,?,?) RETURNING stock_allele_id";
 435     my $sth  = $self->get_schema->storage->dbh->prepare($q);
 436     $sth->execute($self->get_stock_id, $allele_id, $metadata_id);
 437     my ($id) =  $sth->fetchrow_array;
 438     return $id;
 439 }
 440
 441
 442 ##########
 443 1;########
 444 ##########