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 hte 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
  12 use standard DBIC syntax.
  13
  14 =head1 AUTHOR
  15
  16 Naama Menda <nm249@cornell.edu>
  17
  18 =cut
  19
  20 package CXGN::Chado::Stock ;
  21 use strict;
  22 use warnings;
  23 use Carp;
  24 use Bio::Chado::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
  45      ### First, bless the class to create the object and set the schema into the object.
  46     #my $self = $class->SUPER::new($schema);
  47     my $self = bless {}, $class;
  48     $self->set_schema($schema);
  49     my $stock;
  50     if (defined $id) {
  51         $stock = $self->get_resultset('Stock::Stock')->find({ stock_id => $id });
  52     } else {
  53         ### Create an empty resultset object;
  54         $stock = $self->get_resultset('Stock::Stock')->new( {} );
  55     }
  56     ###It's important to set the object row for using the accesor in other class functions
  57     $self->set_object_row($stock);
  58     return $self;
  59 }
  60
  61
  62
  63 =head2 store
  64
  65  Usage: $self->store
  66  Desc:  store a new stock
  67  Ret:   a database id
  68  Args:  none
  69  Side Effects: checks if the stock exists in the database, and if does, will attempt to update
  70  Example:
  71
  72 =cut
  73
  74 sub store {
  75     my $self=shift;
  76     my $id = $self->get_stock_id();
  77     my $schema=$self->get_schema();
  78     #no stock id . Check first if the name  exists in te database
  79     if (!$id) {
  80         my $exists= $self->exists_in_database();
  81         if (!$exists) {
  82             my $new_row = $self->get_object_row();
  83             $new_row->insert();
  84
  85             $id=$new_row->stock_id();
  86         }else {
  87             my $existing_stock=$self->get_resultset('Stock::Stock')->find($exists);
  88             #don't update here if stock already exist. User should call from the code exist_in_database
  89             #and instantiate a new stock object with the database id
  90             #updating here is not a good idea, since it might not be what the user intended to do
  91             #and it can mess up the database.
  92         }
  93     }else { # id exists
  94         $self->get_object_row()->update();
  95     }
  96     return $id
  97 }
  98
  99 ########################
 100
 101
 102 =head2 exists_in_database
 103
 104  Usage: $self->exists_in_database()
 105  Desc:  check if the uniquename exists in the stock table
 106  Ret:
 107  Args:
 108  Side Effects:
 109  Example:
 110
 111 =cut
 112
 113 sub exists_in_database {
 114     my $self=shift;
 115     my $stock_id = $self->get_stock_id();
 116     my $uniquename = $self->get_uniquename || '' ;
 117     my ($s) = $self->get_resultset('Stock::Stock')->search(
 118         {
 119             uniquename  => { 'ilike' => $uniquename },
 120         });
 121     #loading new stock - $stock_id is undef
 122     if (defined($s) && !$stock_id ) {  return $s->stock_id ; }
 123
 124     #updating an existing stock
 125     elsif ($stock_id && defined($s) ) {
 126         if ( ($s->stock_id == $stock_id) ) {
 127             return 0;
 128             #trying to update the uniquename
 129         } elsif ( $s->stock_id != $stock_id ) {
 130             return " Can't update an existing stock $stock_id uniquename:$uniquename.";
 131             # if the new name we're trying to update/insert does not exist in the stock table..
 132         } elsif ($stock_id && !$s->stock_id) {
 133             return 0;
 134         }
 135     }
 136     return undef;
 137 }
 138
 139 =head2 get_organism
 140
 141  Usage: $self->get_organism
 142  Desc:  find the organism object of this stock
 143  Ret:   L<Bio::Chado::Schema::Organism::Organism> object
 144  Args:  none
 145  Side Effects: none
 146  Example:
 147
 148 =cut
 149
 150 sub get_organism {
 151     my $self = shift;
 152     if ($self->get_organism_id) {
 153         return $self->get_object_row()->find_related('organism');
 154     }
 155     return undef;
 156 }
 157
 158 =head2 get_type
 159
 160  Usage: $self->get_type
 161  Desc:  find the cvterm type of this stock
 162  Ret:   L<Bio::Chado::Schema::Cv::Cvterm> object
 163  Args:   none
 164  Side Effects: none
 165  Example:
 166
 167 =cut
 168
 169 sub get_type {
 170     my $self = shift;
 171     if ($self->get_type_id) {
 172         return  $self->get_object_row()->find_related('type');
 173     }
 174     return undef;
 175 }
 176
 177
 178
 179 sub get_object_row {
 180     my $self = shift;
 181     return $self->{object_row};
 182 }
 183
 184 sub set_object_row {
 185   my $self = shift;
 186   $self->{object_row} = shift;
 187 }
 188
 189 =head2 get_resultset
 190
 191  Usage: $self->get_resultset(ModuleName::TableName)
 192  Desc:  Get a ResultSet object for source_name
 193  Ret:   a ResultSet object
 194  Args:  a source name
 195  Side Effects: none
 196  Example:
 197
 198 =cut
 199
 200 sub get_resultset {
 201     my $self=shift;
 202     my $source = shift;
 203     return $self->get_schema()->resultset("$source");
 204 }
 205
 206 =head2 accessors get_schema, set_schema
 207
 208  Usage:
 209  Desc:
 210  Property
 211  Side Effects:
 212  Example:
 213
 214 =cut
 215
 216 sub get_schema {
 217   my $self = shift;
 218   return $self->{schema};
 219 }
 220
 221 sub set_schema {
 222   my $self = shift;
 223   $self->{schema} = shift;
 224 }
 225
 226
 227 ###mapping accessors to DBIC
 228
 229 =head2 accessors get_name, set_name
 230
 231  Usage:
 232  Desc:
 233  Property
 234  Side Effects:
 235  Example:
 236
 237 =cut
 238
 239 sub get_name {
 240     my $self = shift;
 241     return $self->get_object_row()->get_column("name");
 242 }
 243
 244 sub set_name {
 245     my $self = shift;
 246     $self->get_object_row()->set_column(name => shift);
 247 }
 248
 249 =head2 accessors get_uniquename, set_uniquename
 250
 251  Usage:
 252  Desc:
 253  Property
 254  Side Effects:
 255  Example:
 256
 257 =cut
 258
 259 sub get_uniquename {
 260     my $self = shift;
 261     return $self->get_object_row()->get_column("uniquename");
 262 }
 263
 264 sub set_uniquename {
 265     my $self = shift;
 266     $self->get_object_row()->set_column(uniquename => shift);
 267 }
 268
 269 =head2 accessors get_organism_id, set_organism_id
 270
 271  Usage:
 272  Desc:
 273  Property
 274  Side Effects:
 275  Example:
 276
 277 =cut
 278
 279 sub get_organism_id {
 280     my $self = shift;
 281     return $self->get_object_row()->get_column("organism_id");
 282 }
 283
 284 sub set_organism_id {
 285     my $self = shift;
 286     $self->get_object_row()->set_column(organism_id => shift);
 287 }
 288
 289 =head2 accessors get_type_id, set_type_id
 290
 291  Usage:
 292  Desc:
 293  Property
 294  Side Effects:
 295  Example:
 296
 297 =cut
 298
 299 sub get_type_id {
 300     my $self = shift;
 301     return $self->get_object_row()->get_column("type_id");
 302 }
 303
 304 sub set_type_id {
 305     my $self = shift;
 306     $self->get_object_row()->set_column(type_id => shift);
 307 }
 308
 309 =head2 accessors get_description, set_description
 310
 311  Usage:
 312  Desc:
 313  Property
 314  Side Effects:
 315  Example:
 316
 317 =cut
 318
 319 sub get_description {
 320     my $self = shift;
 321     return $self->get_object_row()->get_column("description");
 322 }
 323
 324 sub set_description {
 325     my $self = shift;
 326     $self->get_object_row()->set_column(description => shift);
 327 }
 328
 329 =head2 accessors get_stock_id, set_stock_id
 330
 331  Usage:
 332  Desc:
 333  Property
 334  Side Effects:
 335  Example:
 336
 337 =cut
 338
 339 sub get_stock_id {
 340     my $self = shift;
 341     return $self->get_object_row()->get_column("stock_id");
 342 }
 343
 344 sub set_stock_id {
 345     my $self = shift;
 346     $self->get_object_row()->set_column(stock_id => shift);
 347 }
 348
 349 =head2 accessors get_is_obsolete, set_is_obsolete
 350
 351  Usage:
 352  Desc:
 353  Property
 354  Side Effects:
 355  Example:
 356
 357 =cut
 358
 359 sub get_is_obsolete {
 360     my $self = shift;
 361     return $self->get_object_row()->get_column("is_obsolete");
 362 }
 363
 364 sub set_is_obsolete {
 365     my $self = shift;
 366     $self->get_object_row()->set_column(is_obsolete => shift);
 367 }
 368
 369
 370
 371 ##########
 372 1;########
 373 ##########